printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild openbabel 2>&1 The package 'openbabel' will be built without being installed. Reading build dependency for openbabel-2.2.3-11... Reading dependency for openbabel-2.2.3-11... Reading dependency for libopenbabel3-shlibs-2.2.3-11... Reading dependency for libopenbabel3-dev-2.2.3-11... Reading build conflict for openbabel-2.2.3-11... The package 'autoconf2.6' will be installed. Reading dependency for autoconf2.6-2.69-3... Reading runtime dependency for autoconf2.6-2.69-3... The package 'automake1.11' will be installed. Reading dependency for automake1.11-1.11.6-7... Reading runtime dependency for automake1.11-1.11.6-7... The package 'libiconv-dev' will be installed. Reading dependency for libiconv-dev-1.14-5... Reading runtime dependency for libiconv-dev-1.14-5... The package 'libstdinchi1-dev' will be installed. Reading dependency for libstdinchi1-dev-1.02-2... Reading runtime dependency for libstdinchi1-dev-1.02-2... The package 'libtool2' will be installed. Reading dependency for libtool2-2.4.2-3... Reading runtime dependency for libtool2-2.4.2-3... The package 'libxml2' will be installed. Reading dependency for libxml2-2.9.1-3... Reading runtime dependency for libxml2-2.9.1-3... The package 'libstdinchi1-shlibs' will be installed. Reading dependency for libstdinchi1-shlibs-1.02-2... Reading runtime dependency for libstdinchi1-shlibs-1.02-2... The package 'm4' will be installed. Reading dependency for m4-1.4.17-1... Reading runtime dependency for m4-1.4.17-1... The package 'automake1.11-core' will be installed. Reading dependency for automake1.11-core-1.11.6-7... Reading runtime dependency for automake1.11-core-1.11.6-7... The package 'libtool2-shlibs' will be installed. Reading dependency for libtool2-shlibs-2.4.2-3... Reading runtime dependency for libtool2-shlibs-2.4.2-3... The package 'libxml2-bin' will be installed. Reading dependency for libxml2-bin-2.9.1-3... Reading runtime dependency for libxml2-bin-2.9.1-3... The package 'libxml2-shlibs' will be installed. Reading dependency for libxml2-shlibs-2.9.1-3... Reading runtime dependency for libxml2-shlibs-2.9.1-3... The package 'libsigsegv2-shlibs' will be installed. Reading dependency for libsigsegv2-shlibs-2.6-5... Reading runtime dependency for libsigsegv2-shlibs-2.6-5... The package 'liblzma5-shlibs' will be installed. Reading dependency for liblzma5-shlibs-5.0.5-2... Reading runtime dependency for liblzma5-shlibs-5.0.5-2... The package 'readline6-shlibs' will be installed. Reading dependency for readline6-shlibs-6.3.6-1... Reading runtime dependency for readline6-shlibs-6.3.6-1... The following package will be rebuilt: openbabel The following 15 additional packages will be installed: autoconf2.6 automake1.11 automake1.11-core libiconv-dev liblzma5-shlibs libsigsegv2-shlibs libstdinchi1-dev libstdinchi1-shlibs libtool2 libtool2-shlibs libxml2 libxml2-bin libxml2-shlibs m4 readline6-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/openbabel-2.2.3.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 6468k 1 99667 0 0 83326 0 0:01:19 0:00:01 0:01:18 83333 4 6468k 4 293k 0 0 172k 0 0:00:37 0:00:01 0:00:36 172k 15 6468k 15 981k 0 0 364k 0 0:00:17 0:00:02 0:00:15 364k 21 6468k 21 1388k 0 0 320k 0 0:00:20 0:00:04 0:00:16 320k 27 6468k 27 1763k 0 0 369k 0 0:00:17 0:00:04 0:00:13 369k 37 6468k 37 2424k 0 0 425k 0 0:00:15 0:00:05 0:00:10 517k 50 6468k 50 3264k 0 0 487k 0 0:00:13 0:00:06 0:00:07 594k 64 6468k 64 4169k 0 0 541k 0 0:00:11 0:00:07 0:00:04 637k 76 6468k 76 4939k 0 0 537k 0 0:00:12 0:00:09 0:00:03 731k 81 6468k 81 5284k 0 0 544k 0 0:00:11 0:00:09 0:00:02 712k 91 6468k 91 5897k 0 0 551k 0 0:00:11 0:00:10 0:00:01 693k 100 6468k 100 6468k 0 0 558k 0 0:00:11 0:00:11 --:--:-- 656k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libiconv-dev_1.14-5_darwin-x86_64.deb Selecting previously deselected package libiconv-dev. (Reading database ... 4296 files and directories currently installed.) Unpacking libiconv-dev (from .../libiconv-dev_1.14-5_darwin-x86_64.deb) ... Setting up libiconv-dev (1.14-5) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/utils/liblzma5-shlibs_5.0.5-2_darwin-x86_64.deb Selecting previously deselected package liblzma5-shlibs. (Reading database ... 4314 files and directories currently installed.) Unpacking liblzma5-shlibs (from .../liblzma5-shlibs_5.0.5-2_darwin-x86_64.deb) ... Setting up liblzma5-shlibs (5.0.5-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libsigsegv2-shlibs_2.6-5_darwin-x86_64.deb Selecting previously deselected package libsigsegv2-shlibs. (Reading database ... 4325 files and directories currently installed.) Unpacking libsigsegv2-shlibs (from .../libsigsegv2-shlibs_2.6-5_darwin-x86_64.deb) ... Setting up libsigsegv2-shlibs (2.6-5) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/libstdinchi1-dev_1.02-2_darwin-x86_64.deb /sw/fink/debs/libstdinchi1-shlibs_1.02-2_darwin-x86_64.deb Selecting previously deselected package libstdinchi1-dev. (Reading database ... 4334 files and directories currently installed.) Unpacking libstdinchi1-dev (from .../libstdinchi1-dev_1.02-2_darwin-x86_64.deb) ... Selecting previously deselected package libstdinchi1-shlibs. Unpacking libstdinchi1-shlibs (from .../libstdinchi1-shlibs_1.02-2_darwin-x86_64.deb) ... Setting up libstdinchi1-shlibs (1.02-2) ... Setting up libstdinchi1-dev (1.02-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/libtool2_2.4.2-3_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/libtool2-shlibs_2.4.2-3_darwin-x86_64.deb Selecting previously deselected package libtool2. (Reading database ... 4344 files and directories currently installed.) Unpacking libtool2 (from .../libtool2_2.4.2-3_darwin-x86_64.deb) ... Selecting previously deselected package libtool2-shlibs. Unpacking libtool2-shlibs (from .../libtool2-shlibs_2.4.2-3_darwin-x86_64.deb) ... Setting up libtool2-shlibs (2.4.2-3) ... Setting up libtool2 (2.4.2-3) ... Clearing dependency_libs of .la files being installed * Libtool: (libtool). Generic shared library support script. install-info(/sw/share/info/libtool.info): creating new section `GNU programming tools' Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/m4_1.4.17-1_darwin-x86_64.deb Selecting previously deselected package m4. (Reading database ... 4433 files and directories currently installed.) Unpacking m4 (from .../m4_1.4.17-1_darwin-x86_64.deb) ... Setting up m4 (1.4.17-1) ... * M4: (m4). A powerful macro processor. Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/readline6-shlibs_6.3.6-1_darwin-x86_64.deb Selecting previously deselected package readline6-shlibs. (Reading database ... 4444 files and directories currently installed.) Unpacking readline6-shlibs (from .../readline6-shlibs_6.3.6-1_darwin-x86_64.deb) ... Setting up readline6-shlibs (6.3.6-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/autoconf2.6_2.69-3_darwin-x86_64.deb Selecting previously deselected package autoconf2.6. (Reading database ... 4455 files and directories currently installed.) Unpacking autoconf2.6 (from .../autoconf2.6_2.69-3_darwin-x86_64.deb) ... Setting up autoconf2.6 (2.69-3) ... * Autoconf: (autoconf). Create source code configuration scripts. * Standards: (standards). GNU coding standards. install-info(/sw/share/info/standards.info): creating new section `GNU organization' Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/automake1.11_1.11.6-7_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/automake1.11-core_1.11.6-7_darwin-x86_64.deb Selecting previously deselected package automake1.11. (Reading database ... 4539 files and directories currently installed.) Unpacking automake1.11 (from .../automake1.11_1.11.6-7_darwin-x86_64.deb) ... Selecting previously deselected package automake1.11-core. Unpacking automake1.11-core (from .../automake1.11-core_1.11.6-7_darwin-x86_64.deb) ... Setting up automake1.11-core (1.11.6-7) ... Setting up automake1.11 (1.11.6-7) ... * Automake: (automake). Making GNU standards-compliant Makefiles. Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/libxml2_2.9.1-3_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libxml2-shlibs_2.9.1-3_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libxml2-bin_2.9.1-3_darwin-x86_64.deb Selecting previously deselected package libxml2. (Reading database ... 4690 files and directories currently installed.) Unpacking libxml2 (from .../libxml2_2.9.1-3_darwin-x86_64.deb) ... Selecting previously deselected package libxml2-shlibs. Unpacking libxml2-shlibs (from .../libxml2-shlibs_2.9.1-3_darwin-x86_64.deb) ... Selecting previously deselected package libxml2-bin. Unpacking libxml2-bin (from .../libxml2-bin_2.9.1-3_darwin-x86_64.deb) ... Setting up libxml2-shlibs (2.9.1-3) ... Setting up libxml2-bin (2.9.1-3) ... Setting up libxml2 (2.9.1-3) ... Clearing dependency_libs of .la files being installed Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-openbabel-2.2.3-11 /sw/build.build dpkg-deb: building package `fink-buildlock-openbabel-2.2.3-11' in `/sw/build.build/fink-buildlock-openbabel-2.2.3-11_2014.08.02-03.44.16_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-openbabel-2.2.3-11_2014.08.02-03.44.16_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-openbabel-2.2.3-11. (Reading database ... 5058 files and directories currently installed.) Unpacking fink-buildlock-openbabel-2.2.3-11 (from .../fink-buildlock-openbabel-2.2.3-11_2014.08.02-03.44.16_darwin-x86_64.deb) ... Setting up fink-buildlock-openbabel-2.2.3-11 (2014.08.02-03.44.16) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.6Wr4b env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/openbabel-2.2.3.tar.gz openbabel-2.2.3/ openbabel-2.2.3/acinclude.m4 openbabel-2.2.3/aclocal.m4 openbabel-2.2.3/AUTHORS openbabel-2.2.3/autoconf/ openbabel-2.2.3/autoconf/libtool.m4 openbabel-2.2.3/autoconf/ltoptions.m4 openbabel-2.2.3/autoconf/ltsugar.m4 openbabel-2.2.3/autoconf/ltversion.m4 openbabel-2.2.3/autoconf/lt~obsolete.m4 openbabel-2.2.3/ChangeLog openbabel-2.2.3/cmake/ openbabel-2.2.3/cmake/modules/ openbabel-2.2.3/cmake/modules/MacroEnsureVersion.cmake openbabel-2.2.3/CMakeLists.txt openbabel-2.2.3/config.guess openbabel-2.2.3/config.sub openbabel-2.2.3/configure openbabel-2.2.3/configure.in openbabel-2.2.3/COPYING openbabel-2.2.3/data/ openbabel-2.2.3/data/aromatic.h openbabel-2.2.3/data/aromatic.txt openbabel-2.2.3/data/atomtyp.h openbabel-2.2.3/data/atomtyp.txt openbabel-2.2.3/data/bin2hex.pl openbabel-2.2.3/data/bondtyp.h openbabel-2.2.3/data/bondtyp.txt openbabel-2.2.3/data/CMakeLists.txt openbabel-2.2.3/data/element.h openbabel-2.2.3/data/element.txt openbabel-2.2.3/data/fragments.txt openbabel-2.2.3/data/ghemical.prm openbabel-2.2.3/data/isotope-small.txt openbabel-2.2.3/data/isotope.h openbabel-2.2.3/data/isotope.txt openbabel-2.2.3/data/logp.txt openbabel-2.2.3/data/MACCS.txt openbabel-2.2.3/data/Makefile.am openbabel-2.2.3/data/Makefile.in openbabel-2.2.3/data/mmff94.ff openbabel-2.2.3/data/mmff94s.ff openbabel-2.2.3/data/mmffang.par openbabel-2.2.3/data/mmffbndk.par openbabel-2.2.3/data/mmffbond.par openbabel-2.2.3/data/mmffchg.par openbabel-2.2.3/data/mmffdef.par openbabel-2.2.3/data/mmffdfsb.par openbabel-2.2.3/data/mmffoop.par openbabel-2.2.3/data/mmffpbci.par openbabel-2.2.3/data/mmffprop.par openbabel-2.2.3/data/mmffs_oop.par openbabel-2.2.3/data/mmffs_tor.par openbabel-2.2.3/data/mmffstbn.par openbabel-2.2.3/data/mmfftor.par openbabel-2.2.3/data/mmffvdw.par openbabel-2.2.3/data/mr.txt openbabel-2.2.3/data/patterns.txt openbabel-2.2.3/data/phmodel.txt openbabel-2.2.3/data/phmodeldata.h openbabel-2.2.3/data/plugindefines.txt openbabel-2.2.3/data/psa.txt openbabel-2.2.3/data/resdata.h openbabel-2.2.3/data/resdata.txt openbabel-2.2.3/data/ringtyp.txt openbabel-2.2.3/data/SMARTS_InteLigand.txt openbabel-2.2.3/data/space-groups.txt openbabel-2.2.3/data/torlib.h openbabel-2.2.3/data/torlib.txt openbabel-2.2.3/data/types.h openbabel-2.2.3/data/types.txt openbabel-2.2.3/data/UFF.prm openbabel-2.2.3/depcomp openbabel-2.2.3/doc/ openbabel-2.2.3/doc/babel.1 openbabel-2.2.3/doc/babel.html openbabel-2.2.3/doc/babel31.inc openbabel-2.2.3/doc/CMakeLists.txt openbabel-2.2.3/doc/dioxin.inc openbabel-2.2.3/doc/dioxin.mol2 openbabel-2.2.3/doc/dioxin.png openbabel-2.2.3/doc/dioxin.pov openbabel-2.2.3/doc/FAQ.html openbabel-2.2.3/doc/Makefile.am openbabel-2.2.3/doc/Makefile.in openbabel-2.2.3/doc/obchiral.1 openbabel-2.2.3/doc/obchiral.html openbabel-2.2.3/doc/obconformer.1 openbabel-2.2.3/doc/obconformer.html openbabel-2.2.3/doc/obenergy.1 openbabel-2.2.3/doc/obenergy.html openbabel-2.2.3/doc/obfit.1 openbabel-2.2.3/doc/obfit.html openbabel-2.2.3/doc/obgen.1 openbabel-2.2.3/doc/obgen.html openbabel-2.2.3/doc/obgrep.1 openbabel-2.2.3/doc/obgrep.html openbabel-2.2.3/doc/obminimize.1 openbabel-2.2.3/doc/obminimize.html openbabel-2.2.3/doc/obprobe.1 openbabel-2.2.3/doc/obprobe.html openbabel-2.2.3/doc/obprop.1 openbabel-2.2.3/doc/obprop.html openbabel-2.2.3/doc/obrotamer.1 openbabel-2.2.3/doc/obrotamer.html openbabel-2.2.3/doc/obrotate.1 openbabel-2.2.3/doc/obrotate.html openbabel-2.2.3/doc/OBTwoMigration.html openbabel-2.2.3/doc/README.dioxin.pov openbabel-2.2.3/doc/README.povray openbabel-2.2.3/doc/roundtrip.1 openbabel-2.2.3/Doxyfile openbabel-2.2.3/include/ openbabel-2.2.3/include/chemdrawcdx.h openbabel-2.2.3/include/CMakeLists.txt openbabel-2.2.3/include/inchi102/ openbabel-2.2.3/include/inchi102/aux2atom.h openbabel-2.2.3/include/inchi102/extr_ct.h openbabel-2.2.3/include/inchi102/ichi.h openbabel-2.2.3/include/inchi102/ichi_bns.h openbabel-2.2.3/include/inchi102/ichi_io.h openbabel-2.2.3/include/inchi102/ichicano.h openbabel-2.2.3/include/inchi102/ichicant.h openbabel-2.2.3/include/inchi102/ichicomn.h openbabel-2.2.3/include/inchi102/ichicomp.h openbabel-2.2.3/include/inchi102/ichidrp.h openbabel-2.2.3/include/inchi102/ichierr.h openbabel-2.2.3/include/inchi102/ichimain.h openbabel-2.2.3/include/inchi102/ichimake.h openbabel-2.2.3/include/inchi102/ichinorm.h openbabel-2.2.3/include/inchi102/ichiparm.h openbabel-2.2.3/include/inchi102/ichiring.h openbabel-2.2.3/include/inchi102/ichirvrs.h openbabel-2.2.3/include/inchi102/ichisize.h openbabel-2.2.3/include/inchi102/ichister.h openbabel-2.2.3/include/inchi102/ichitaut.h openbabel-2.2.3/include/inchi102/ichitime.h openbabel-2.2.3/include/inchi102/ikey_base26.h openbabel-2.2.3/include/inchi102/inchi_api.h openbabel-2.2.3/include/inchi102/inchi_dll_a.h openbabel-2.2.3/include/inchi102/inchi_dll_main.h openbabel-2.2.3/include/inchi102/inchicmp.h openbabel-2.2.3/include/inchi102/incomdef.h openbabel-2.2.3/include/inchi102/inpdef.h openbabel-2.2.3/include/inchi102/lreadmol.h openbabel-2.2.3/include/inchi102/mode.h openbabel-2.2.3/include/inchi102/sha2.h openbabel-2.2.3/include/inchi102/strutil.h openbabel-2.2.3/include/inchi102/util.h openbabel-2.2.3/include/inchi_api.h openbabel-2.2.3/include/Makefile.am openbabel-2.2.3/include/Makefile.in openbabel-2.2.3/include/OB-BGL/ openbabel-2.2.3/include/OB-BGL/example.cpp openbabel-2.2.3/include/OB-BGL/mol_graph.h openbabel-2.2.3/include/OB-BGL/verbose_visitors.h openbabel-2.2.3/include/openbabel/ openbabel-2.2.3/include/openbabel/alias.h openbabel-2.2.3/include/openbabel/atom.h openbabel-2.2.3/include/openbabel/atomclass.h openbabel-2.2.3/include/openbabel/base.h openbabel-2.2.3/include/openbabel/bitvec.h openbabel-2.2.3/include/openbabel/bond.h openbabel-2.2.3/include/openbabel/bondtyper.h openbabel-2.2.3/include/openbabel/builder.h openbabel-2.2.3/include/openbabel/canon.h openbabel-2.2.3/include/openbabel/chains.h openbabel-2.2.3/include/openbabel/chiral.h openbabel-2.2.3/include/openbabel/data.h openbabel-2.2.3/include/openbabel/descriptor.h openbabel-2.2.3/include/openbabel/dlhandler.h openbabel-2.2.3/include/openbabel/fingerprint.h openbabel-2.2.3/include/openbabel/forcefield.h openbabel-2.2.3/include/openbabel/format.h openbabel-2.2.3/include/openbabel/generic.h openbabel-2.2.3/include/openbabel/grid.h openbabel-2.2.3/include/openbabel/griddata.h openbabel-2.2.3/include/openbabel/groupcontrib.h openbabel-2.2.3/include/openbabel/internalcoord.h openbabel-2.2.3/include/openbabel/kinetics.h openbabel-2.2.3/include/openbabel/lineend.h openbabel-2.2.3/include/openbabel/locale.h openbabel-2.2.3/include/openbabel/Makefile.am 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openbabel-2.2.3/test/conversion.cpp openbabel-2.2.3/test/data.cpp openbabel-2.2.3/test/ffghemical.cpp openbabel-2.2.3/test/ffmmff94.cpp openbabel-2.2.3/test/ffuff.cpp openbabel-2.2.3/test/files/ openbabel-2.2.3/test/files/3d.head.2.cml openbabel-2.2.3/test/files/aromatics.smi openbabel-2.2.3/test/files/attype.00.smi openbabel-2.2.3/test/files/filterset.sdf openbabel-2.2.3/test/files/forcefield.sdf openbabel-2.2.3/test/files/formalchargeresults.txt openbabel-2.2.3/test/files/formularesults.txt openbabel-2.2.3/test/files/FormulaTest.smi openbabel-2.2.3/test/files/ghemicalresults.txt openbabel-2.2.3/test/files/invalid-smarts.txt openbabel-2.2.3/test/files/invalid-smiles.txt openbabel-2.2.3/test/files/mmff94results.txt openbabel-2.2.3/test/files/nci.smi openbabel-2.2.3/test/files/random openbabel-2.2.3/test/files/random2 openbabel-2.2.3/test/files/random3 openbabel-2.2.3/test/files/ringresults.txt openbabel-2.2.3/test/files/smartsresults.txt openbabel-2.2.3/test/files/smartstest.txt openbabel-2.2.3/test/files/stripresults.txt openbabel-2.2.3/test/files/test2d.xyz openbabel-2.2.3/test/files/test3d.xyz openbabel-2.2.3/test/files/uffresults.txt openbabel-2.2.3/test/files/unitcell.txt openbabel-2.2.3/test/files/unitcell_results.txt openbabel-2.2.3/test/files/ziptest.sdf.gz openbabel-2.2.3/test/formalcharge.cpp openbabel-2.2.3/test/format.cpp openbabel-2.2.3/test/formula.cpp openbabel-2.2.3/test/inchi/ openbabel-2.2.3/test/inchi/Samples.sdf openbabel-2.2.3/test/inchi/Samples.txt openbabel-2.2.3/test/inchi/SamplesTechMan.sdf openbabel-2.2.3/test/inchi/SamplesTechMan.txt openbabel-2.2.3/test/inchi.pl openbabel-2.2.3/test/inchi2.pl openbabel-2.2.3/test/inchiwrite.cpp openbabel-2.2.3/test/internalcoord.cpp openbabel-2.2.3/test/invalidsmarts.cpp openbabel-2.2.3/test/invalidsmiles.cpp openbabel-2.2.3/test/iterators.cpp openbabel-2.2.3/test/logp_psa.cpp openbabel-2.2.3/test/Makefile.am openbabel-2.2.3/test/Makefile.in openbabel-2.2.3/test/math.cpp openbabel-2.2.3/test/mol.cpp openbabel-2.2.3/test/phmodel.cpp openbabel-2.2.3/test/README openbabel-2.2.3/test/residue.cpp openbabel-2.2.3/test/ringtest.cpp openbabel-2.2.3/test/roundtrip.cpp openbabel-2.2.3/test/smartstest.cpp openbabel-2.2.3/test/smilesmatch.cpp openbabel-2.2.3/test/strip.cpp openbabel-2.2.3/test/test-set.sh openbabel-2.2.3/test/unitcell.cpp openbabel-2.2.3/test/wrapper.sh openbabel-2.2.3/test/zipstream.cpp openbabel-2.2.3/THANKS openbabel-2.2.3/tools/ openbabel-2.2.3/tools/babel.cpp openbabel-2.2.3/tools/CMakeLists.txt openbabel-2.2.3/tools/Makefile.am openbabel-2.2.3/tools/Makefile.in openbabel-2.2.3/tools/obchiral.cpp openbabel-2.2.3/tools/obconformer.cpp openbabel-2.2.3/tools/obenergy.cpp openbabel-2.2.3/tools/obfit.cpp openbabel-2.2.3/tools/obgen.cpp openbabel-2.2.3/tools/obgrep.cpp openbabel-2.2.3/tools/obminimize.cpp openbabel-2.2.3/tools/obprobe.cpp openbabel-2.2.3/tools/obprop.cpp openbabel-2.2.3/tools/obrotamer.cpp openbabel-2.2.3/tools/obrotate.cpp openbabel-2.2.3/tools/obsym.cpp openbabel-2.2.3/tools/README openbabel-2.2.3/windows-vc2005/ openbabel-2.2.3/windows-vc2005/Add2D/ openbabel-2.2.3/windows-vc2005/Add2D/Add2D.vcproj openbabel-2.2.3/windows-vc2005/babelconfig.h openbabel-2.2.3/windows-vc2005/Distribution/ openbabel-2.2.3/windows-vc2005/Distribution/CheckInstallerScript.py openbabel-2.2.3/windows-vc2005/Distribution/ExampleFiles/ openbabel-2.2.3/windows-vc2005/Distribution/ExampleFiles/150mols.smi openbabel-2.2.3/windows-vc2005/Distribution/ExampleFiles/FourSmallMols.cml openbabel-2.2.3/windows-vc2005/Distribution/ExampleFiles/oxamide.cml openbabel-2.2.3/windows-vc2005/Distribution/ExampleFiles/serotonin.mol openbabel-2.2.3/windows-vc2005/Distribution/logo_big.bmp openbabel-2.2.3/windows-vc2005/Distribution/logo_small.bmp openbabel-2.2.3/windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi openbabel-2.2.3/windows-vc2005/Distribution/ToolsPrograms.txt openbabel-2.2.3/windows-vc2005/examples/ openbabel-2.2.3/windows-vc2005/examples/benzene.sdf openbabel-2.2.3/windows-vc2005/examples/example1.cpp openbabel-2.2.3/windows-vc2005/examples/example1.vcproj openbabel-2.2.3/windows-vc2005/gen3D/ openbabel-2.2.3/windows-vc2005/gen3D/gen3D.vcproj openbabel-2.2.3/windows-vc2005/iconv.dll openbabel-2.2.3/windows-vc2005/libstdinchi.dll openbabel-2.2.3/windows-vc2005/libstdinchi.lib openbabel-2.2.3/windows-vc2005/libxml2.dll openbabel-2.2.3/windows-vc2005/libxml2.lib openbabel-2.2.3/windows-vc2005/OBComLn/ openbabel-2.2.3/windows-vc2005/OBComLn/OBComLn.vcproj openbabel-2.2.3/windows-vc2005/OBCommonFormats/ openbabel-2.2.3/windows-vc2005/OBCommonFormats/OBCommonFormats.vcproj openbabel-2.2.3/windows-vc2005/OBConsole/ openbabel-2.2.3/windows-vc2005/OBConsole/OBConsole.vcproj openbabel-2.2.3/windows-vc2005/OBConv/ openbabel-2.2.3/windows-vc2005/OBConv/OBConv.vcproj openbabel-2.2.3/windows-vc2005/OBCSharp/ openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/ openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/AtomExtensions.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/DotBabel.csproj openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/DotBabel.csproj.user openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/MathExtensions.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/OBConvert.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/OBDescriptor.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/OBMolExtensions.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/OBReader.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/OBWriter.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/Properties/ openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/Properties/AssemblyInfo.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/Smiles.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/Tools.cs openbabel-2.2.3/windows-vc2005/OBCSharp/DotBabel/Transform.cs openbabel-2.2.3/windows-vc2005/OBCSharp/IronPython_Instructions.txt openbabel-2.2.3/windows-vc2005/OBCSharp/OBCSharp.vcproj openbabel-2.2.3/windows-vc2005/OBCSharp/OBCSharpBindings.sln openbabel-2.2.3/windows-vc2005/OBCSharp/OBCSharpBindings.suo openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/ openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/bin/ openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/bin/Release/ openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/OBDotNet.csproj openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/OBDotNet.csproj.user openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/Properties/ openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/Properties/obdotnet.snk openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNet/Properties/OBDotNetAssemblyInfo.cs openbabel-2.2.3/windows-vc2005/OBCSharp/obdotnet.bat openbabel-2.2.3/windows-vc2005/OBCSharp/obdotnet.snk openbabel-2.2.3/windows-vc2005/OBCSharp/OBDotNetAssemblyInfo.txt openbabel-2.2.3/windows-vc2005/OBDESC/ openbabel-2.2.3/windows-vc2005/OBDESC/OBDESC.vcproj openbabel-2.2.3/windows-vc2005/OBDLL/ openbabel-2.2.3/windows-vc2005/OBDLL/OBDLL.vcproj openbabel-2.2.3/windows-vc2005/OBError/ openbabel-2.2.3/windows-vc2005/OBError/OBError.vcproj openbabel-2.2.3/windows-vc2005/OBFPRT/ openbabel-2.2.3/windows-vc2005/OBFPRT/OBFPRT.vcproj openbabel-2.2.3/windows-vc2005/OBFS/ openbabel-2.2.3/windows-vc2005/OBFS/OBFS.vcproj openbabel-2.2.3/windows-vc2005/OBGUI/ openbabel-2.2.3/windows-vc2005/OBGUI/OBGUI.vcproj openbabel-2.2.3/windows-vc2005/OBGUI/OpenBabelGUI.html openbabel-2.2.3/windows-vc2005/OBGUI.exe.manifest openbabel-2.2.3/windows-vc2005/OBGUII/ openbabel-2.2.3/windows-vc2005/OBGUII/OBGUII.vcproj openbabel-2.2.3/windows-vc2005/OBGUII/OpenBabelGUI.html openbabel-2.2.3/windows-vc2005/OBInchi/ openbabel-2.2.3/windows-vc2005/OBInchi/OBInchi.vcproj openbabel-2.2.3/windows-vc2005/OBJava/ openbabel-2.2.3/windows-vc2005/OBJava/objava.bat openbabel-2.2.3/windows-vc2005/OBJava/OBJava.vcproj openbabel-2.2.3/windows-vc2005/OBJava/org/ openbabel-2.2.3/windows-vc2005/OBJava/org/openbabel/ openbabel-2.2.3/windows-vc2005/OBMCDL/ openbabel-2.2.3/windows-vc2005/OBMCDL/MCDL.vcproj openbabel-2.2.3/windows-vc2005/OBMoreFormats/ openbabel-2.2.3/windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj openbabel-2.2.3/windows-vc2005/OBPythonOBF/ openbabel-2.2.3/windows-vc2005/OBPythonOBF/logo.bmp openbabel-2.2.3/windows-vc2005/OBPythonOBF/obpython.bat openbabel-2.2.3/windows-vc2005/OBPythonOBF/OBPythonOBF.vcproj openbabel-2.2.3/windows-vc2005/OBPythonOBF/Readme.txt openbabel-2.2.3/windows-vc2005/OBPythonOBF/setup.py openbabel-2.2.3/windows-vc2005/OBTools/ openbabel-2.2.3/windows-vc2005/OBTools/nbabel.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obchiral.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obconformer.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obenergy.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obfit.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obminimize.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obmm.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obprobe.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obprop.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obrotamer.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obrotate.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obseq.vcproj openbabel-2.2.3/windows-vc2005/OBTools/obsym.vcproj openbabel-2.2.3/windows-vc2005/OBTools/Projects in OBTools.txt openbabel-2.2.3/windows-vc2005/OBTools.sln openbabel-2.2.3/windows-vc2005/OBUtilFormats/ openbabel-2.2.3/windows-vc2005/OBUtilFormats/OBUtilFormats.vcproj openbabel-2.2.3/windows-vc2005/OBXMLFormats/ openbabel-2.2.3/windows-vc2005/OBXMLFormats/OBXMLFormats.vcproj openbabel-2.2.3/windows-vc2005/OpenBabelDLL/ openbabel-2.2.3/windows-vc2005/OpenBabelDLL/OpenBabelDLL.vcproj openbabel-2.2.3/windows-vc2005/OpenBabelOBF.sln openbabel-2.2.3/windows-vc2005/Projects in this workspace.txt openbabel-2.2.3/windows-vc2005/setenv.txt openbabel-2.2.3/windows-vc2005/template/ openbabel-2.2.3/windows-vc2005/template/template.cpp openbabel-2.2.3/windows-vc2005/template/template.vcproj openbabel-2.2.3/windows-vc2005/zdll.lib openbabel-2.2.3/windows-vc2005/zlib1.dll openbabel-2.2.3/windows-vc2005/zlib1.lib sudo -u fink-bld [ENV] sh -c /tmp/fink.nouKp [ -r /sw/fink/dists/stable/main/finkinfo/sci/openbabel-2.2.3.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.Ymltk patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/openbabel-2.2.3.patch patching file configure.in patching file src/formats/Makefile.am sudo -u fink-bld [ENV] sh -c /tmp/fink.gsC77 autoreconf -fi main::scan_file() called too early to check prototype at /sw/bin/aclocal line 643. configure.in:198: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from... autoconf/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... autoconf/libtool.m4:4158: _LT_LINKER_SHLIBS is expanded from... autoconf/libtool.m4:5233: _LT_LANG_C_CONFIG is expanded from... autoconf/libtool.m4:138: _LT_SETUP is expanded from... autoconf/libtool.m4:67: LT_INIT is expanded from... autoconf/libtool.m4:103: AM_PROG_LIBTOOL is expanded from... configure.in:198: the top level configure.in:198: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from... autoconf/libtool.m4:4158: _LT_LINKER_SHLIBS is expanded from... autoconf/libtool.m4:5233: _LT_LANG_C_CONFIG is expanded from... autoconf/libtool.m4:138: _LT_SETUP is expanded from... autoconf/libtool.m4:67: LT_INIT is expanded from... autoconf/libtool.m4:103: AM_PROG_LIBTOOL is expanded from... configure.in:198: the top level configure.in:198: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from... autoconf/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... autoconf/libtool.m4:5340: _LT_LANG_CXX_CONFIG is expanded from... autoconf/libtool.m4:785: _LT_LANG is expanded from... autoconf/libtool.m4:768: LT_LANG is expanded from... autoconf/libtool.m4:796: _LT_LANG_DEFAULT_CONFIG is expanded from... autoconf/libtool.m4:138: _LT_SETUP is expanded from... autoconf/libtool.m4:67: LT_INIT is expanded from... autoconf/libtool.m4:103: AM_PROG_LIBTOOL is expanded from... configure.in:198: the top level configure.in:298: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... configure.in:298: the top level configure.in:198: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from... autoconf/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... autoconf/libtool.m4:4158: _LT_LINKER_SHLIBS is expanded from... autoconf/libtool.m4:5233: _LT_LANG_C_CONFIG is expanded from... autoconf/libtool.m4:138: _LT_SETUP is expanded from... autoconf/libtool.m4:67: LT_INIT is expanded from... autoconf/libtool.m4:103: AM_PROG_LIBTOOL is expanded from... configure.in:198: the top level configure.in:198: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from... autoconf/libtool.m4:4158: _LT_LINKER_SHLIBS is expanded from... autoconf/libtool.m4:5233: _LT_LANG_C_CONFIG is expanded from... autoconf/libtool.m4:138: _LT_SETUP is expanded from... autoconf/libtool.m4:67: LT_INIT is expanded from... autoconf/libtool.m4:103: AM_PROG_LIBTOOL is expanded from... configure.in:198: the top level configure.in:198: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from... autoconf/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... autoconf/libtool.m4:5340: _LT_LANG_CXX_CONFIG is expanded from... autoconf/libtool.m4:785: _LT_LANG is expanded from... autoconf/libtool.m4:768: LT_LANG is expanded from... autoconf/libtool.m4:796: _LT_LANG_DEFAULT_CONFIG is expanded from... autoconf/libtool.m4:138: _LT_SETUP is expanded from... autoconf/libtool.m4:67: LT_INIT is expanded from... autoconf/libtool.m4:103: AM_PROG_LIBTOOL is expanded from... configure.in:198: the top level configure.in:298: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... configure.in:298: the top level libtoolize: putting auxiliary files in `.'. libtoolize: copying file `./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `autoconf'. libtoolize: copying file `autoconf/libtool.m4' libtoolize: copying file `autoconf/ltoptions.m4' libtoolize: copying file `autoconf/ltsugar.m4' libtoolize: copying file `autoconf/ltversion.m4' libtoolize: copying file `autoconf/lt~obsolete.m4' libtoolize: Consider adding `-I autoconf' to ACLOCAL_AMFLAGS in Makefile.am. main::scan_file() called too early to check prototype at /sw/bin/aclocal line 643. configure.in:298: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... configure.in:298: the top level configure.in:298: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... configure.in:298: the top level configure.in:298: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... configure.in:298: the top level configure.in:298: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... configure.in:298: the top level mv include/inchi_api.h include/inchi_api.h_UNUSED ./configure --prefix=/sw --enable-shared --enable-dependency-tracking --mandir=/sw/share/man --disable-inchi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking auto silent in maintainer mode... auto-sleep-9 checking build system type... x86_64-apple-darwin13.3.0 checking host system type... x86_64-apple-darwin13.3.0 checking for style of include used by make... GNU checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for boostlib >= 1.33.1... configure: Boost not found checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for doxygen... no checking for swig... no checking for perl... /usr/bin/perl checking for prove... /usr/bin/prove checking for python... /usr/bin/python checking for ruby... /usr/bin/ruby checking for gmcs... no checking for javac... /usr/bin/javac checking for jar... /usr/bin/jar checking for wx-config... no configure: WARNING: Cannot find doxygen to build documentation. Have a look at http://www.doxygen.org/ checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin13.3.0 file names to x86_64-apple-darwin13.3.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.3.0 file names to toolchain format... func_convert_file_noop checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... dlltool checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking whether byte ordering is bigendian... no checking for asin in -lm... yes checking for dlopen in -lc... yes checking for xml2-config... /sw/bin/xml2-config checking for libxml - version >= 2.6.5... yes (version 2.9.1) checking for GetStdINCHI in -lstdinchi... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for stdlib.h... (cached) yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking conio.h usability... no checking conio.h presence... no checking for conio.h... no checking for string.h... (cached) yes checking strstream.h usability... no checking strstream.h presence... no checking for strstream.h... no checking iostream.h usability... no checking iostream.h presence... no checking for iostream.h... no checking fstream.h usability... no checking fstream.h presence... no checking for fstream.h... no checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking iostream usability... yes checking iostream presence... yes checking for iostream... yes checking fstream usability... yes checking fstream presence... yes checking for fstream... yes checking sstream usability... yes checking sstream presence... yes checking for sstream... yes checking strstream usability... yes checking strstream presence... yes checking for strstream... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking tr1/memory usability... no checking tr1/memory presence... no checking for tr1/memory... no checking rpc/types.h usability... yes checking rpc/types.h presence... yes checking for rpc/types.h... yes checking for rpc/xdr.h... yes checking xlocale.h usability... yes checking xlocale.h presence... yes checking for xlocale.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking whether time.h and sys/time.h may both be included... yes checking for clock_t... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for rint... yes checking for sranddev... yes checking for uselocale... yes checking for snprintf... yes checking for strncasecmp... yes checking whether scandir needs a const cast... yes configure: creating ./config.status config.status: creating Makefile config.status: creating data/Makefile config.status: creating src/Makefile config.status: creating src/math/Makefile config.status: creating src/formats/Makefile config.status: creating src/fingerprints/Makefile config.status: creating src/formats/xml/Makefile config.status: creating src/formats/inchi102/Makefile config.status: creating src/forcefields/Makefile config.status: creating src/GUI/Makefile config.status: creating src/descriptors/Makefile config.status: creating src/ops/Makefile config.status: creating include/Makefile config.status: creating include/openbabel/Makefile config.status: creating include/openbabel/math/Makefile config.status: creating test/Makefile config.status: creating test/cmltest/Makefile config.status: creating tools/Makefile config.status: creating doc/Makefile config.status: creating scripts/Makefile config.status: creating openbabel-2.0.pc config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing include/openbabel/babelconfig.h commands make Making all in data /Applications/Xcode.app/Contents/Developer/usr/bin/make all-am make[2]: Nothing to be done for `all-am'. Making all in src /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in math /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT matrix3x3.lo -MD -MP -MF .deps/matrix3x3.Tpo -c -o matrix3x3.lo matrix3x3.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT vector3.lo -MD -MP -MF .deps/vector3.Tpo -c -o vector3.lo vector3.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT transform3d.lo -MD -MP -MF .deps/transform3d.Tpo -c -o transform3d.lo transform3d.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT spacegroup.lo -MD -MP -MF .deps/spacegroup.Tpo -c -o spacegroup.lo spacegroup.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT transform3d.lo -MD -MP -MF .deps/transform3d.Tpo -c transform3d.cpp -fno-common -DPIC -o .libs/transform3d.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT spacegroup.lo -MD -MP -MF .deps/spacegroup.Tpo -c spacegroup.cpp -fno-common -DPIC -o .libs/spacegroup.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT vector3.lo -MD -MP -MF .deps/vector3.Tpo -c vector3.cpp -fno-common -DPIC -o .libs/vector3.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT matrix3x3.lo -MD -MP -MF .deps/matrix3x3.Tpo -c matrix3x3.cpp -fno-common -DPIC -o .libs/matrix3x3.o mv -f .deps/vector3.Tpo .deps/vector3.Plo mv -f .deps/matrix3x3.Tpo .deps/matrix3x3.Plo mv -f .deps/transform3d.Tpo .deps/transform3d.Plo mv -f .deps/spacegroup.Tpo .deps/spacegroup.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o libmath.la matrix3x3.lo vector3.lo transform3d.lo spacegroup.lo -lz -lm libtool: link: ar cru .libs/libmath.a .libs/matrix3x3.o .libs/vector3.o .libs/transform3d.o .libs/spacegroup.o libtool: link: ranlib .libs/libmath.a libtool: link: ( cd ".libs" && rm -f "libmath.la" && ln -s "../libmath.la" "libmath.la" ) Making all in fingerprints /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT finger2.lo -MD -MP -MF .deps/finger2.Tpo -c -o finger2.lo finger2.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT finger3.lo -MD -MP -MF .deps/finger3.Tpo -c -o finger3.lo finger3.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT finger3.lo -MD -MP -MF .deps/finger3.Tpo -c finger3.cpp -fno-common -DPIC -o .libs/finger3.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT finger2.lo -MD -MP -MF .deps/finger2.Tpo -c finger2.cpp -fno-common -DPIC -o .libs/finger2.o finger3.cpp:220:34: warning: unsequenced modification and access to 'div' [-Wunsequenced] ngrp = (num + div -1)/div--; //rounds up ~~~ ^ mv -f .deps/finger2.Tpo .deps/finger2.Plo 1 warning generated. mv -f .deps/finger3.Tpo .deps/finger3.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o libfingerprints.la finger2.lo finger3.lo -lz -lm libtool: link: ar cru .libs/libfingerprints.a .libs/finger2.o .libs/finger3.o libtool: link: ranlib .libs/libfingerprints.a libtool: link: ( cd ".libs" && rm -f "libfingerprints.la" && ln -s "../libfingerprints.la" "libfingerprints.la" ) Making all in forcefields /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../include -I/sw/include -Wall -g -O2 -MT forcefieldghemical.lo -MD -MP -MF .deps/forcefieldghemical.Tpo -c -o forcefieldghemical.lo forcefieldghemical.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../include -I/sw/include -Wall -g -O2 -MT forcefieldmmff94.lo -MD -MP -MF .deps/forcefieldmmff94.Tpo -c -o forcefieldmmff94.lo forcefieldmmff94.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../include -I/sw/include -Wall -g -O2 -MT forcefielduff.lo -MD -MP -MF .deps/forcefielduff.Tpo -c -o forcefielduff.lo forcefielduff.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../include -I/sw/include -Wall -g -O2 -MT forcefielduff.lo -MD -MP -MF .deps/forcefielduff.Tpo -c forcefielduff.cpp -fno-common -DPIC -o .libs/forcefielduff.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../include -I/sw/include -Wall -g -O2 -MT forcefieldmmff94.lo -MD -MP -MF .deps/forcefieldmmff94.Tpo -c forcefieldmmff94.cpp -fno-common -DPIC -o .libs/forcefieldmmff94.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../include -I/sw/include -Wall -g -O2 -MT forcefieldghemical.lo -MD -MP -MF .deps/forcefieldghemical.Tpo -c forcefieldghemical.cpp -fno-common -DPIC -o .libs/forcefieldghemical.o In file included from forcefielduff.cpp:24: In file included from ./forcefielduff.h:24: In file included from ../../include/openbabel/forcefield.h:32: ../../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] In file included from forcefieldghemical.cpp:23: In file included from ./forcefieldghemical.h:23: In file included from ../../include/openbabel/forcefield.h:32: ../../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ void Init(OBMol &box,double spacing, double pad=0.0); ^ ../../include/openbabel/grid.h:55:18:../../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from forcefieldghemical.cpp:23: In file included from ./forcefieldghemical.h:23: In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] In file included from forcefielduff.cpp:24: In file included from ./forcefielduff.h:24: In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h double GetValue(int i, int j, int k) const; ^ :74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] ../../include/openbabel/base.h:206:32 double GetValue(int i, int j, int k) const; : ^ note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const../../include/openbabel/base.h :206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) ^ In file included from forcefieldghemical.cpp:23 virtual const std::string &GetValue() const: In file included from ^./forcefieldghemical.h :23: In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h:In file included from 76forcefielduff.cpp:24: In file included from ./forcefielduff.h:24: :12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../../include/openbabel/base.h: double GetValue (vector3 pos) const;206 :32 ^: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ virtual const std::string &GetValue() const ^ forcefieldghemical.cpp:1117:71: warning: '&&' within '||' [-Wlogical-op-parentheses] ((_a == parameter[idx]._b) && (_b == parameter[idx]._a)) && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ forcefieldghemical.cpp:1117:71: note: place parentheses around the '&&' expression to silence this warning ((_a == parameter[idx]._b) && (_b == parameter[idx]._a)) && ^ In file included from forcefieldmmff94.cpp:36: In file included from ./forcefieldmmff94.h:24: In file included from ../../include/openbabel/forcefield.h:32: ../../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from forcefieldmmff94.cpp:36: In file included from ./forcefieldmmff94.h:24: In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from forcefieldmmff94.cpp:36: In file included from ./forcefieldmmff94.h:24: In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ forcefieldmmff94.cpp:3247:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else { ^ forcefieldmmff94.cpp:3679:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((o_count + s_count) == 3) ^ forcefieldmmff94.cpp:3687:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((o_count + s_count) == 3) ^ forcefieldmmff94.cpp:3827:15: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else if ((type == _ffchgparams[idx].b) && (nbr_type == _ffchgparams[idx].a)) { ^ forcefieldmmff94.cpp:4423:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ forcefieldmmff94.cpp:4428:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ forcefieldmmff94.cpp:4444:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ forcefieldmmff94.cpp:4449:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ forcefieldmmff94.cpp:4459:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ forcefieldmmff94.cpp:4464:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ forcefieldmmff94.cpp:4904:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 4 warnings generated. 3 warnings generated. mv -f .deps/forcefielduff.Tpo .deps/forcefielduff.Plo mv -f .deps/forcefieldghemical.Tpo .deps/forcefieldghemical.Plo 14 warnings generated. mv -f .deps/forcefieldmmff94.Tpo .deps/forcefieldmmff94.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o libforcefields.la forcefieldghemical.lo forcefieldmmff94.lo forcefielduff.lo -lz -lm libtool: link: ar cru .libs/libforcefields.a .libs/forcefieldghemical.o .libs/forcefieldmmff94.o .libs/forcefielduff.o libtool: link: ranlib .libs/libforcefields.a libtool: link: ( cd ".libs" && rm -f "libforcefields.la" && ln -s "../libforcefields.la" "libforcefields.la" ) Making all in descriptors /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT cmpdfilter.lo -MD -MP -MF .deps/cmpdfilter.Tpo -c -o cmpdfilter.lo cmpdfilter.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT filters.lo -MD -MP -MF .deps/filters.Tpo -c -o filters.lo filters.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT groupcontrib.lo -MD -MP -MF .deps/groupcontrib.Tpo -c -o groupcontrib.lo groupcontrib.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT smartsdescriptors.lo -MD -MP -MF .deps/smartsdescriptors.Tpo -c -o smartsdescriptors.lo smartsdescriptors.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT smartsdescriptors.lo -MD -MP -MF .deps/smartsdescriptors.Tpo -c smartsdescriptors.cpp -fno-common -DPIC -o .libs/smartsdescriptors.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT filters.lo -MD -MP -MF .deps/filters.Tpo -c filters.cpp -fno-common -DPIC -o .libs/filters.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT groupcontrib.lo -MD -MP -MF .deps/groupcontrib.Tpo -c groupcontrib.cpp -fno-common -DPIC -o .libs/groupcontrib.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT cmpdfilter.lo -MD -MP -MF .deps/cmpdfilter.Tpo -c cmpdfilter.cpp -fno-common -DPIC -o .libs/cmpdfilter.o mv -f .deps/cmpdfilter.Tpo .deps/cmpdfilter.Plo mv -f .deps/smartsdescriptors.Tpo .deps/smartsdescriptors.Plo mv -f .deps/filters.Tpo .deps/filters.Plo mv -f .deps/groupcontrib.Tpo .deps/groupcontrib.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o libdescriptors.la cmpdfilter.lo filters.lo groupcontrib.lo smartsdescriptors.lo -lz -lm libtool: link: ar cru .libs/libdescriptors.a .libs/cmpdfilter.o .libs/filters.o .libs/groupcontrib.o .libs/smartsdescriptors.o libtool: link: ranlib .libs/libdescriptors.a libtool: link: ( cd ".libs" && rm -f "libdescriptors.la" && ln -s "../libdescriptors.la" "libdescriptors.la" ) Making all in ops /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT addpolarh.lo -MD -MP -MF .deps/addpolarh.Tpo -c -o addpolarh.lo addpolarh.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT gen3d.lo -MD -MP -MF .deps/gen3d.Tpo -c -o gen3d.lo gen3d.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT loader.lo -MD -MP -MF .deps/loader.Tpo -c -o loader.lo loader.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT optransform.lo -MD -MP -MF .deps/optransform.Tpo -c -o optransform.lo optransform.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT fillUC.lo -MD -MP -MF .deps/fillUC.Tpo -c -o fillUC.lo fillUC.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT gen3d.lo -MD -MP -MF .deps/gen3d.Tpo -c gen3d.cpp -fno-common -DPIC -o .libs/gen3d.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT addpolarh.lo -MD -MP -MF .deps/addpolarh.Tpo -c addpolarh.cpp -fno-common -DPIC -o .libs/addpolarh.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT optransform.lo -MD -MP -MF .deps/optransform.Tpo -c optransform.cpp -fno-common -DPIC -o .libs/optransform.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT loader.lo -MD -MP -MF .deps/loader.Tpo -c loader.cpp -fno-common -DPIC -o .libs/loader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../src -I../../include -I/sw/include -Wall -g -O2 -MT fillUC.lo -MD -MP -MF .deps/fillUC.Tpo -c fillUC.cpp -fno-common -DPIC -o .libs/fillUC.o In file included from gen3d.cpp:23: In file included from ../../include/openbabel/forcefield.h:32: ../../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from gen3d.cpp:23: In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from gen3d.cpp:23: In file included from ../../include/openbabel/forcefield.h:33: ../../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ loader.cpp:127:15: warning: private field '_filename' is not used [-Wunused-private-field] const char* _filename; ^ loader.cpp:128:15: warning: private field '_descr' is not used [-Wunused-private-field] const char* _descr; ^ 3 warnings generated. mv -f .deps/gen3d.Tpo .deps/gen3d.Plo mv -f .deps/addpolarh.Tpo .deps/addpolarh.Plo 2 warnings generated. mv -f .deps/loader.Tpo .deps/loader.Plo mv -f .deps/fillUC.Tpo .deps/fillUC.Plo mv -f .deps/optransform.Tpo .deps/optransform.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o libops.la addpolarh.lo gen3d.lo loader.lo optransform.lo fillUC.lo -lz -lm libtool: link: ar cru .libs/libops.a .libs/addpolarh.o .libs/gen3d.o .libs/loader.o .libs/optransform.o .libs/fillUC.o libtool: link: ranlib .libs/libops.a libtool: link: ( cd ".libs" && rm -f "libops.la" && ln -s "../libops.la" "libops.la" ) Making all in . /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT alias.lo -MD -MP -MF .deps/alias.Tpo -c -o alias.lo alias.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT base.lo -MD -MP -MF .deps/base.Tpo -c -o base.lo base.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT bitvec.lo -MD -MP -MF .deps/bitvec.Tpo -c -o bitvec.lo bitvec.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT bond.lo -MD -MP -MF .deps/bond.Tpo -c -o bond.lo bond.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT bondtyper.lo -MD -MP -MF .deps/bondtyper.Tpo -c -o bondtyper.lo bondtyper.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT canon.lo -MD -MP -MF .deps/canon.Tpo -c -o canon.lo canon.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT builder.lo -MD -MP -MF .deps/builder.Tpo -c -o builder.lo builder.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.cpp -fno-common -DPIC -o .libs/atom.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT alias.lo -MD -MP -MF .deps/alias.Tpo -c alias.cpp -fno-common -DPIC -o .libs/alias.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT base.lo -MD -MP -MF .deps/base.Tpo -c base.cpp -fno-common -DPIC -o .libs/base.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT bond.lo -MD -MP -MF .deps/bond.Tpo -c bond.cpp -fno-common -DPIC -o .libs/bond.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT bitvec.lo -MD -MP -MF .deps/bitvec.Tpo -c bitvec.cpp -fno-common -DPIC -o .libs/bitvec.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT builder.lo -MD -MP -MF .deps/builder.Tpo -c builder.cpp -fno-common -DPIC -o .libs/builder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT bondtyper.lo -MD -MP -MF .deps/bondtyper.Tpo -c bondtyper.cpp -fno-common -DPIC -o .libs/bondtyper.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT canon.lo -MD -MP -MF .deps/canon.Tpo -c canon.cpp -fno-common -DPIC -o .libs/canon.o mv -f .deps/base.Tpo .deps/base.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT chains.lo -MD -MP -MF .deps/chains.Tpo -c -o chains.lo chains.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT chains.lo -MD -MP -MF .deps/chains.Tpo -c chains.cpp -fno-common -DPIC -o .libs/chains.o mv -f .deps/alias.Tpo .deps/alias.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT chiral.lo -MD -MP -MF .deps/chiral.Tpo -c -o chiral.lo chiral.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT chiral.lo -MD -MP -MF .deps/chiral.Tpo -c chiral.cpp -fno-common -DPIC -o .libs/chiral.o mv -f .deps/bitvec.Tpo .deps/bitvec.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT data.lo -MD -MP -MF .deps/data.Tpo -c -o data.lo data.cpp builder.cpp:596:9: warning: unused variable 'bondOrder1' [-Wunused-variable] int bondOrder1 = bond1->GetBondOrder(); ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT data.lo -MD -MP -MF .deps/data.Tpo -c data.cpp -fno-common -DPIC -o .libs/data.o mv -f .deps/bond.Tpo .deps/bond.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT descriptor.lo -MD -MP -MF .deps/descriptor.Tpo -c -o descriptor.lo descriptor.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT descriptor.lo -MD -MP -MF .deps/descriptor.Tpo -c descriptor.cpp -fno-common -DPIC -o .libs/descriptor.o mv -f .deps/bondtyper.Tpo .deps/bondtyper.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT fingerprint.lo -MD -MP -MF .deps/fingerprint.Tpo -c -o fingerprint.lo fingerprint.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT fingerprint.lo -MD -MP -MF .deps/fingerprint.Tpo -c fingerprint.cpp -fno-common -DPIC -o .libs/fingerprint.o descriptor.cpp:264:8: warning: unused variable 'error' [-Wunused-variable] bool error=false; ^ 1 warning generated. mv -f .deps/builder.Tpo .deps/builder.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT forcefield.lo -MD -MP -MF .deps/forcefield.Tpo -c -o forcefield.lo forcefield.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT forcefield.lo -MD -MP -MF .deps/forcefield.Tpo -c forcefield.cpp -fno-common -DPIC -o .libs/forcefield.o mv -f .deps/atom.Tpo .deps/atom.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT format.lo -MD -MP -MF .deps/format.Tpo -c -o format.lo format.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT format.lo -MD -MP -MF .deps/format.Tpo -c format.cpp -fno-common -DPIC -o .libs/format.o 1 warning generated. mv -f .deps/descriptor.Tpo .deps/descriptor.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT generic.lo -MD -MP -MF .deps/generic.Tpo -c -o generic.lo generic.cpp mv -f .deps/canon.Tpo .deps/canon.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT griddata.lo -MD -MP -MF .deps/griddata.Tpo -c -o griddata.lo griddata.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT generic.lo -MD -MP -MF .deps/generic.Tpo -c generic.cpp -fno-common -DPIC -o .libs/generic.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT griddata.lo -MD -MP -MF .deps/griddata.Tpo -c griddata.cpp -fno-common -DPIC -o .libs/griddata.o fingerprint.cpp:161:48: warning: unsequenced modification and access to 'ppat' [-Wunsequenced] if ( (a=((*ppat) & (*p++)) ^ (*ppat++)) ) break; ~~~~ ^ In file included from griddata.cpp:25: ../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from griddata.cpp:25: ../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ mv -f .deps/format.Tpo .deps/format.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT grid.lo -MD -MP -MF .deps/grid.Tpo -c -o grid.lo grid.cpp In file included from forcefield.cpp:65: In file included from ../include/openbabel/forcefield.h:32: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from forcefield.cpp:65: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from forcefield.cpp:65: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT grid.lo -MD -MP -MF .deps/grid.Tpo -c grid.cpp -fno-common -DPIC -o .libs/grid.o In file included from griddata.cpp:27: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ forcefield.cpp:1538:9: warning: unused variable 'confCount' [-Wunused-variable] int confCount = 0; ^ generic.cpp:711:5: warning: field '_pointGroup' will be initialized after field '_spaceGroup' [-Wreorder] _pointGroup(src._pointGroup), _spaceGroup(src._spaceGroup) ^ forcefield.cpp:2556:9: warning: unused variable '_ncoords' [-Wunused-variable] int _ncoords = _mol.NumAtoms() * 3; ^ forcefield.cpp:3294:12: warning: unused variable 'kB' [-Wunused-variable] double kB = 0.00831451 / KCAL_TO_KJ; // kcal/(mol*K) ^ mv -f .deps/chiral.Tpo .deps/chiral.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT locale.lo -MD -MP -MF .deps/locale.Tpo -c -o locale.lo locale.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT locale.lo -MD -MP -MF .deps/locale.Tpo -c locale.cpp -fno-common -DPIC -o .libs/locale.o 3 warnings generated. mv -f .deps/griddata.Tpo .deps/griddata.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT kekulize.lo -MD -MP -MF .deps/kekulize.Tpo -c -o kekulize.lo kekulize.cpp 1 warning generated. mv -f .deps/fingerprint.Tpo .deps/fingerprint.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT kekulize.lo -MD -MP -MF .deps/kekulize.Tpo -c kekulize.cpp -fno-common -DPIC -o .libs/kekulize.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cpp -fno-common -DPIC -o .libs/matrix.o mv -f .deps/chains.Tpo .deps/chains.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT mol.lo -MD -MP -MF .deps/mol.Tpo -c -o mol.lo mol.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT mol.lo -MD -MP -MF .deps/mol.Tpo -c mol.cpp -fno-common -DPIC -o .libs/mol.o mv -f .deps/locale.Tpo .deps/locale.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT molchrg.lo -MD -MP -MF .deps/molchrg.Tpo -c -o molchrg.lo molchrg.cpp In file included from grid.cpp:24: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT molchrg.lo -MD -MP -MF .deps/molchrg.Tpo -c molchrg.cpp -fno-common -DPIC -o .libs/molchrg.o grid.cpp:258:9: warning: unused variable 'size' [-Wunused-variable] int size = _xdim*_ydim*_zdim; ^ mv -f .deps/data.Tpo .deps/data.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obconversion.lo -MD -MP -MF .deps/obconversion.Tpo -c -o obconversion.lo obconversion.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obconversion.lo -MD -MP -MF .deps/obconversion.Tpo -c obconversion.cpp -fno-common -DPIC -o .libs/obconversion.o kekulize.cpp:318:20: warning: unused variable 'atom2' [-Wunused-variable] OBAtom *atom, *atom2; ^ mv -f .deps/matrix.Tpo .deps/matrix.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT oberror.lo -MD -MP -MF .deps/oberror.Tpo -c -o oberror.lo oberror.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT oberror.lo -MD -MP -MF .deps/oberror.Tpo -c oberror.cpp -fno-common -DPIC -o .libs/oberror.o 2 warnings generated. mv -f .deps/grid.Tpo .deps/grid.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obiter.lo -MD -MP -MF .deps/obiter.Tpo -c -o obiter.lo obiter.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obiter.lo -MD -MP -MF .deps/obiter.Tpo -c obiter.cpp -fno-common -DPIC -o .libs/obiter.o mol.cpp:3573:27: warning: '&&' within '||' [-Wlogical-op-parentheses] && (((atom->GetBond(b))->GetLength() < shortestBond) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mol.cpp:3573:27: note: place parentheses around the '&&' expression to silence this warning && (((atom->GetBond(b))->GetLength() < shortestBond) ^ obconversion.cpp:208:17: warning: field 'pAuxConv' will be initialized after field 'pLineEndBuf' [-Wreorder] pOb1(NULL), pAuxConv(NULL),pLineEndBuf(NULL),wInpos(0),wInlen(0) ^ mol.cpp:3901:9: warning: unused variable 'fragments' [-Wunused-variable] int fragments = 0; ^ obconversion.cpp:1048:10: warning: unused variable 'ret' [-Wunused-variable] bool ret=true; ^ mv -f .deps/molchrg.Tpo .deps/molchrg.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obmolecformat.lo -MD -MP -MF .deps/obmolecformat.Tpo -c -o obmolecformat.lo obmolecformat.cpp 1 warning generated. mv -f .deps/generic.Tpo .deps/generic.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obutil.lo -MD -MP -MF .deps/obutil.Tpo -c -o obutil.lo obutil.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obmolecformat.lo -MD -MP -MF .deps/obmolecformat.Tpo -c obmolecformat.cpp -fno-common -DPIC -o .libs/obmolecformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT obutil.lo -MD -MP -MF .deps/obutil.Tpo -c obutil.cpp -fno-common -DPIC -o .libs/obutil.o 1 warning generated. mv -f .deps/kekulize.Tpo .deps/kekulize.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT op.lo -MD -MP -MF .deps/op.Tpo -c -o op.lo op.cpp mol.cpp:2217:15: warning: function 'KekulePropagate' is not needed and will not be emitted [-Wunneeded-internal-declaration] static bool KekulePropagate(OBAtom *atom,vector &visit,vector &ival,int depth) ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT op.lo -MD -MP -MF .deps/op.Tpo -c op.cpp -fno-common -DPIC -o .libs/op.o mv -f .deps/oberror.Tpo .deps/oberror.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT ops.lo -MD -MP -MF .deps/ops.Tpo -c -o ops.lo ops.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT ops.lo -MD -MP -MF .deps/ops.Tpo -c ops.cpp -fno-common -DPIC -o .libs/ops.o mv -f .deps/op.Tpo .deps/op.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT parsmart.lo -MD -MP -MF .deps/parsmart.Tpo -c -o parsmart.lo parsmart.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT parsmart.lo -MD -MP -MF .deps/parsmart.Tpo -c parsmart.cpp -fno-common -DPIC -o .libs/parsmart.o 6 warnings generated. mv -f .deps/forcefield.Tpo .deps/forcefield.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT patty.lo -MD -MP -MF .deps/patty.Tpo -c -o patty.lo patty.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT patty.lo -MD -MP -MF .deps/patty.Tpo -c patty.cpp -fno-common -DPIC -o .libs/patty.o 2 warnings generated. mv -f .deps/obconversion.Tpo .deps/obconversion.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT phmodel.lo -MD -MP -MF .deps/phmodel.Tpo -c -o phmodel.lo phmodel.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT phmodel.lo -MD -MP -MF .deps/phmodel.Tpo -c phmodel.cpp -fno-common -DPIC -o .libs/phmodel.o mv -f .deps/ops.Tpo .deps/ops.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT plugin.lo -MD -MP -MF .deps/plugin.Tpo -c -o plugin.lo plugin.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT plugin.lo -MD -MP -MF .deps/plugin.Tpo -c plugin.cpp -fno-common -DPIC -o .libs/plugin.o mv -f .deps/obiter.Tpo .deps/obiter.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT pointgroup.lo -MD -MP -MF .deps/pointgroup.Tpo -c -o pointgroup.lo pointgroup.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT pointgroup.lo -MD -MP -MF .deps/pointgroup.Tpo -c pointgroup.cpp -fno-common -DPIC -o .libs/pointgroup.o mv -f .deps/obmolecformat.Tpo .deps/obmolecformat.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT rand.lo -MD -MP -MF .deps/rand.Tpo -c -o rand.lo rand.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT rand.lo -MD -MP -MF .deps/rand.Tpo -c rand.cpp -fno-common -DPIC -o .libs/rand.o mv -f .deps/obutil.Tpo .deps/obutil.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT residue.lo -MD -MP -MF .deps/residue.Tpo -c -o residue.lo residue.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT residue.lo -MD -MP -MF .deps/residue.Tpo -c residue.cpp -fno-common -DPIC -o .libs/residue.o mv -f .deps/plugin.Tpo .deps/plugin.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT ring.lo -MD -MP -MF .deps/ring.Tpo -c -o ring.lo ring.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT ring.lo -MD -MP -MF .deps/ring.Tpo -c ring.cpp -fno-common -DPIC -o .libs/ring.o patty.cpp:264:13: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if (failOnUndefined) ^~~~~~~~~~~~~~~ patty.cpp:277:12: note: uninitialized use occurs here return(result); ^~~~~~ patty.cpp:264:9: note: remove the 'if' if its condition is always false if (failOnUndefined) ^~~~~~~~~~~~~~~~~~~~ patty.cpp:233:15: note: initialize the variable 'result' to silence this warning int result; ^ = 0 In file included from rand.cpp:31: ../include/openbabel/rand.h:73:18: warning: private field 'i' is not used [-Wunused-private-field] unsigned int i; ^ parsmart.cpp:2613:19: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if (r3 == -1) ^ parsmart.cpp:2622:19: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if (r3 == -1) ^ 1 warning generated. mv -f .deps/rand.Tpo .deps/rand.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT rotor.lo -MD -MP -MF .deps/rotor.Tpo -c -o rotor.lo rotor.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT rotor.lo -MD -MP -MF .deps/rotor.Tpo -c rotor.cpp -fno-common -DPIC -o .libs/rotor.o parsmart.cpp:2303:20: warning: function 'NotAtomExpr' is not needed and will not be emitted [-Wunneeded-internal-declaration] static AtomExpr *NotAtomExpr( AtomExpr *expr ) ^ 3 warnings generated. mv -f .deps/mol.Tpo .deps/mol.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT rotamer.lo -MD -MP -MF .deps/rotamer.Tpo -c -o rotamer.lo rotamer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT rotamer.lo -MD -MP -MF .deps/rotamer.Tpo -c rotamer.cpp -fno-common -DPIC -o .libs/rotamer.o 1 warning generated. mv -f .deps/patty.Tpo .deps/patty.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT tokenst.lo -MD -MP -MF .deps/tokenst.Tpo -c -o tokenst.lo tokenst.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT tokenst.lo -MD -MP -MF .deps/tokenst.Tpo -c tokenst.cpp -fno-common -DPIC -o .libs/tokenst.o mv -f .deps/phmodel.Tpo .deps/phmodel.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT typer.lo -MD -MP -MF .deps/typer.Tpo -c -o typer.lo typer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT typer.lo -MD -MP -MF .deps/typer.Tpo -c typer.cpp -fno-common -DPIC -o .libs/typer.o pointgroup.cpp:1124:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if( axis->direction[2] < 0 ) ^ pointgroup.cpp:1121:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if( axis->direction[1] <= 0 ) ^ mv -f .deps/residue.Tpo .deps/residue.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT transform.lo -MD -MP -MF .deps/transform.Tpo -c -o transform.lo transform.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT transform.lo -MD -MP -MF .deps/transform.Tpo -c transform.cpp -fno-common -DPIC -o .libs/transform.o mv -f .deps/tokenst.Tpo .deps/tokenst.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT dlhandler_unix.lo -MD -MP -MF .deps/dlhandler_unix.Tpo -c -o dlhandler_unix.lo dlhandler_unix.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../include -I../data/ -I../include -DOB_MODULE_PATH=\"/sw/lib/openbabel/2.2.3\" -DUSING_DYNAMIC_LIBS -I/sw/include -Wall -g -O2 -MT dlhandler_unix.lo -MD -MP -MF .deps/dlhandler_unix.Tpo -c dlhandler_unix.cpp -fno-common -DPIC -o .libs/dlhandler_unix.o 3 warnings generated. mv -f .deps/parsmart.Tpo .deps/parsmart.Plo 2 warnings generated. mv -f .deps/pointgroup.Tpo .deps/pointgroup.Plo mv -f .deps/ring.Tpo .deps/ring.Plo rotamer.cpp:89:14: warning: unused variable 'SwabInt' [-Wunused-const-variable] const bool SwabInt = (STPTR[0]!=0); ^ mv -f .deps/dlhandler_unix.Tpo .deps/dlhandler_unix.Plo mv -f .deps/transform.Tpo .deps/transform.Plo 1 warning generated. mv -f .deps/rotamer.Tpo .deps/rotamer.Plo mv -f .deps/typer.Tpo .deps/typer.Plo mv -f .deps/rotor.Tpo .deps/rotor.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -version-info 3:3:0 -no-undefined -L/sw/lib -o libopenbabel.la -rpath /sw/lib atom.lo alias.lo base.lo bitvec.lo bond.lo bondtyper.lo canon.lo builder.lo chains.lo chiral.lo data.lo descriptor.lo fingerprint.lo forcefield.lo format.lo generic.lo griddata.lo grid.lo locale.lo kekulize.lo matrix.lo mol.lo molchrg.lo obconversion.lo oberror.lo obiter.lo obmolecformat.lo obutil.lo op.lo ops.lo parsmart.lo patty.lo phmodel.lo plugin.lo pointgroup.lo rand.lo residue.lo ring.lo rotor.lo rotamer.lo tokenst.lo typer.lo transform.lo dlhandler_unix.lo math/libmath.la fingerprints/libfingerprints.la forcefields/libforcefields.la ops/libops.la descriptors/libdescriptors.la -lz -lm libtool: link: g++ -dynamiclib -o .libs/libopenbabel.3.dylib .libs/atom.o .libs/alias.o .libs/base.o .libs/bitvec.o .libs/bond.o .libs/bondtyper.o .libs/canon.o .libs/builder.o .libs/chains.o .libs/chiral.o .libs/data.o .libs/descriptor.o .libs/fingerprint.o .libs/forcefield.o .libs/format.o .libs/generic.o .libs/griddata.o .libs/grid.o .libs/locale.o .libs/kekulize.o .libs/matrix.o .libs/mol.o .libs/molchrg.o .libs/obconversion.o .libs/oberror.o .libs/obiter.o .libs/obmolecformat.o .libs/obutil.o .libs/op.o .libs/ops.o .libs/parsmart.o .libs/patty.o .libs/phmodel.o .libs/plugin.o .libs/pointgroup.o .libs/rand.o .libs/residue.o .libs/ring.o .libs/rotor.o .libs/rotamer.o .libs/tokenst.o .libs/typer.o .libs/transform.o .libs/dlhandler_unix.o -Wl,-force_load,math/.libs/libmath.a -Wl,-force_load,fingerprints/.libs/libfingerprints.a -Wl,-force_load,forcefields/.libs/libforcefields.a -Wl,-force_load,ops/.libs/libops.a -Wl,-force_load,descriptors/.libs/libdescriptors.a -L/sw/lib -lz -lm -O2 -install_name /sw/lib/libopenbabel.3.dylib -compatibility_version 4 -current_version 4.3 -Wl,-single_module libtool: link: (cd ".libs" && rm -f "libopenbabel.dylib" && ln -s "libopenbabel.3.dylib" "libopenbabel.dylib") libtool: link: ( cd ".libs" && rm -f "libopenbabel.la" && ln -s "../libopenbabel.la" "libopenbabel.la" ) Making all in formats /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in xml /bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT pubchem.lo -MD -MP -MF .deps/pubchem.Tpo -c -o pubchem.lo pubchem.cpp /bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT xml.lo -MD -MP -MF .deps/xml.Tpo -c -o xml.lo xml.cpp /bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT xmlformat.lo -MD -MP -MF .deps/xmlformat.Tpo -c -o xmlformat.lo xmlformat.cpp /bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT cdxmlformat.lo -MD -MP -MF .deps/cdxmlformat.Tpo -c -o cdxmlformat.lo cdxmlformat.cpp /bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT cmlformat.lo -MD -MP -MF .deps/cmlformat.Tpo -c -o cmlformat.lo cmlformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT cdxmlformat.lo -MD -MP -MF .deps/cdxmlformat.Tpo -c cdxmlformat.cpp -fno-common -DPIC -o .libs/cdxmlformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT xml.lo -MD -MP -MF .deps/xml.Tpo -c xml.cpp -fno-common -DPIC -o .libs/xml.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT pubchem.lo -MD -MP -MF .deps/pubchem.Tpo -c pubchem.cpp -fno-common -DPIC -o .libs/pubchem.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT cmlformat.lo -MD -MP -MF .deps/cmlformat.Tpo -c cmlformat.cpp -fno-common -DPIC -o .libs/cmlformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../../src -I../../../include -I../../../include -I/sw/include/libxml2 -I/sw/include -I/sw/include -Wall -g -O2 -MT xmlformat.lo -MD -MP -MF .deps/xmlformat.Tpo -c xmlformat.cpp -fno-common -DPIC -o .libs/xmlformat.o xml.cpp:146:22: warning: initialization of pointer of type 'OpenBabel::XMLConversion *' to null from a constant boolean expression [-Wbool-conversion] return false; ^~~~~ cmlformat.cpp:567:23: warning: '&&' within '||' [-Wlogical-op-parentheses] if(using3 && attrname=="x3" || using2 && attrname=="x2" || usingFract && attrname=="xFract") ~~~~~~~^~~~~~~~~~~~~~~~~ ~~ cmlformat.cpp:567:23: note: place parentheses around the '&&' expression to silence this warning if(using3 && attrname=="x3" || using2 && attrname=="x2" || usingFract && attrname=="xFract") ^ ( ) cmlformat.cpp:567:51: warning: '&&' within '||' [-Wlogical-op-parentheses] if(using3 && attrname=="x3" || using2 && attrname=="x2" || usingFract && attrname=="xFract") ~~ ~~~~~~~^~~~~~~~~~~~~~~~~ cmlformat.cpp:567:51: note: place parentheses around the '&&' expression to silence this warning if(using3 && attrname=="x3" || using2 && attrname=="x2" || usingFract && attrname=="xFract") ^ ( ) cmlformat.cpp:567:83: warning: '&&' within '||' [-Wlogical-op-parentheses] if(using3 && attrname=="x3" || using2 && attrname=="x2" || usingFract && attrname=="xFract") ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ cmlformat.cpp:567:83: note: place parentheses around the '&&' expression to silence this warning if(using3 && attrname=="x3" || using2 && attrname=="x2" || usingFract && attrname=="xFract") ^ ( ) cmlformat.cpp:569:28: warning: '&&' within '||' [-Wlogical-op-parentheses] else if(using3 && attrname=="y3" || using2 && attrname=="y2" || usingFract && attrname=="yFract") ~~~~~~~^~~~~~~~~~~~~~~~~ ~~ cmlformat.cpp:569:28: note: place parentheses around the '&&' expression to silence this warning else if(using3 && attrname=="y3" || using2 && attrname=="y2" || usingFract && attrname=="yFract") ^ ( ) cmlformat.cpp:569:56: warning: '&&' within '||' [-Wlogical-op-parentheses] else if(using3 && attrname=="y3" || using2 && attrname=="y2" || usingFract && attrname=="yFract") ~~ ~~~~~~~^~~~~~~~~~~~~~~~~ cmlformat.cpp:569:56: note: place parentheses around the '&&' expression to silence this warning else if(using3 && attrname=="y3" || using2 && attrname=="y2" || usingFract && attrname=="yFract") ^ ( ) cmlformat.cpp:569:88: warning: '&&' within '||' [-Wlogical-op-parentheses] else if(using3 && attrname=="y3" || using2 && attrname=="y2" || usingFract && attrname=="yFract") ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ cmlformat.cpp:569:88: note: place parentheses around the '&&' expression to silence this warning else if(using3 && attrname=="y3" || using2 && attrname=="y2" || usingFract && attrname=="yFract") ^ ( ) cmlformat.cpp:571:28: warning: '&&' within '||' [-Wlogical-op-parentheses] else if(using3 && attrname=="z3" || using2 && attrname=="z2" || usingFract && attrname=="zFract") ~~~~~~~^~~~~~~~~~~~~~~~~ ~~ cmlformat.cpp:571:28: note: place parentheses around the '&&' expression to silence this warning else if(using3 && attrname=="z3" || using2 && attrname=="z2" || usingFract && attrname=="zFract") ^ ( ) cmlformat.cpp:571:56: warning: '&&' within '||' [-Wlogical-op-parentheses] else if(using3 && attrname=="z3" || using2 && attrname=="z2" || usingFract && attrname=="zFract") ~~ ~~~~~~~^~~~~~~~~~~~~~~~~ cmlformat.cpp:571:56: note: place parentheses around the '&&' expression to silence this warning else if(using3 && attrname=="z3" || using2 && attrname=="z2" || usingFract && attrname=="zFract") ^ ( ) cmlformat.cpp:571:88: warning: '&&' within '||' [-Wlogical-op-parentheses] else if(using3 && attrname=="z3" || using2 && attrname=="z2" || usingFract && attrname=="zFract") ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ cmlformat.cpp:571:88: note: place parentheses around the '&&' expression to silence this warning else if(using3 && attrname=="z3" || using2 && attrname=="z2" || usingFract && attrname=="zFract") ^ ( ) cmlformat.cpp:2010:26: warning: unused variable 'C_SCALAR' [-Wunused-variable] static const xmlChar C_SCALAR[] = "scalar"; ^ mv -f .deps/xmlformat.Tpo .deps/xmlformat.Plo 1 warning generated. mv -f .deps/xml.Tpo .deps/xml.Plo mv -f .deps/pubchem.Tpo .deps/pubchem.Plo /bin/sh ../../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined -lz -lm -L/sw/lib -lxml2 -lz -lpthread -L/sw/lib -liconv -lm ../../libopenbabel.la -L/sw/lib -o xmlformat.la -rpath /sw/lib/openbabel/2.2.3 xmlformat.lo xml.lo -lz -lm /bin/sh ../../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined -lz -lm -L/sw/lib -lxml2 -lz -lpthread -L/sw/lib -liconv -lm ../../libopenbabel.la -L/sw/lib -o pubchem.la -rpath /sw/lib/openbabel/2.2.3 pubchem.lo xml.lo -lz -lm mv -f .deps/cdxmlformat.Tpo .deps/cdxmlformat.Plo /bin/sh ../../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined -lz -lm -L/sw/lib -lxml2 -lz -lpthread -L/sw/lib -liconv -lm ../../libopenbabel.la -L/sw/lib -o cdxmlformat.la -rpath /sw/lib/openbabel/2.2.3 cdxmlformat.lo xml.lo -lz -lm cmlformat.cpp:139:54: warning: private field 'TransformsNeeded' is not used [-Wunused-private-field] int CrystalScalarsNeeded, PropertyScalarsNeeded, TransformsNeeded; ^ libtool: link: g++ -o .libs/pubchem.so -bundle .libs/pubchem.o .libs/xml.o -L/sw/lib /sw/lib/libxml2.dylib -lpthread /sw/lib/libiconv.dylib ../../.libs/libopenbabel.dylib -lz -lm -O2 -pthread libtool: link: g++ -o .libs/xmlformat.so -bundle .libs/xmlformat.o .libs/xml.o -L/sw/lib /sw/lib/libxml2.dylib -lpthread /sw/lib/libiconv.dylib ../../.libs/libopenbabel.dylib -lz -lm -O2 -pthread libtool: link: g++ -o .libs/cdxmlformat.so -bundle .libs/cdxmlformat.o .libs/xml.o -L/sw/lib /sw/lib/libxml2.dylib -lpthread /sw/lib/libiconv.dylib ../../.libs/libopenbabel.dylib -lz -lm -O2 -pthread clang: warning: argument unused during compilation: '-pthread' clang: warning: argument unused during compilation: '-pthread' clang: warning: argument unused during compilation: '-pthread' libtool: link: ( cd ".libs" && rm -f "xmlformat.la" && ln -s "../xmlformat.la" "xmlformat.la" ) libtool: link: ( cd ".libs" && rm -f "cdxmlformat.la" && ln -s "../cdxmlformat.la" "cdxmlformat.la" ) libtool: link: ( cd ".libs" && rm -f "pubchem.la" && ln -s "../pubchem.la" "pubchem.la" ) 11 warnings generated. mv -f .deps/cmlformat.Tpo .deps/cmlformat.Plo /bin/sh ../../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined -lz -lm -L/sw/lib -lxml2 -lz -lpthread -L/sw/lib -liconv -lm ../../libopenbabel.la -L/sw/lib -o cmlformat.la -rpath /sw/lib/openbabel/2.2.3 cmlformat.lo xml.lo -lz -lm libtool: link: g++ -o .libs/cmlformat.so -bundle .libs/cmlformat.o .libs/xml.o -L/sw/lib /sw/lib/libxml2.dylib -lpthread /sw/lib/libiconv.dylib ../../.libs/libopenbabel.dylib -lz -lm -O2 -pthread clang: warning: argument unused during compilation: '-pthread' libtool: link: ( cd ".libs" && rm -f "cmlformat.la" && ln -s "../cmlformat.la" "cmlformat.la" ) /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT APIInterface.lo -MD -MP -MF .deps/APIInterface.Tpo -c -o APIInterface.lo APIInterface.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT CSRformat.lo -MD -MP -MF .deps/CSRformat.Tpo -c -o CSRformat.lo CSRformat.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT PQSformat.lo -MD -MP -MF .deps/PQSformat.Tpo -c -o PQSformat.lo PQSformat.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT MCDLformat.lo -MD -MP -MF .deps/MCDLformat.Tpo -c -o MCDLformat.lo MCDLformat.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT alchemyformat.lo -MD -MP -MF .deps/alchemyformat.Tpo -c -o alchemyformat.lo alchemyformat.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT acrformat.lo -MD -MP -MF .deps/acrformat.Tpo -c -o acrformat.lo acrformat.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT adfformat.lo -MD -MP -MF .deps/adfformat.Tpo -c -o adfformat.lo adfformat.cpp /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT ArrayList.lo -MD -MP -MF .deps/ArrayList.Tpo -c -o ArrayList.lo ArrayList.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT ArrayList.lo -MD -MP -MF .deps/ArrayList.Tpo -c ArrayList.c -fno-common -DPIC -o .libs/ArrayList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT adfformat.lo -MD -MP -MF .deps/adfformat.Tpo -c adfformat.cpp -fno-common -DPIC -o .libs/adfformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT acrformat.lo -MD -MP -MF .deps/acrformat.Tpo -c acrformat.cpp -fno-common -DPIC -o .libs/acrformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT CSRformat.lo -MD -MP -MF .deps/CSRformat.Tpo -c CSRformat.cpp -fno-common -DPIC -o .libs/CSRformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT APIInterface.lo -MD -MP -MF .deps/APIInterface.Tpo -c APIInterface.cpp -fno-common -DPIC -o .libs/APIInterface.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT MCDLformat.lo -MD -MP -MF .deps/MCDLformat.Tpo -c MCDLformat.cpp -fno-common -DPIC -o .libs/MCDLformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT PQSformat.lo -MD -MP -MF .deps/PQSformat.Tpo -c PQSformat.cpp -fno-common -DPIC -o .libs/PQSformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT alchemyformat.lo -MD -MP -MF .deps/alchemyformat.Tpo -c alchemyformat.cpp -fno-common -DPIC -o .libs/alchemyformat.o mv -f .deps/ArrayList.Tpo .deps/ArrayList.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT amberformat.lo -MD -MP -MF .deps/amberformat.Tpo -c -o amberformat.lo amberformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT amberformat.lo -MD -MP -MF .deps/amberformat.Tpo -c amberformat.cpp -fno-common -DPIC -o .libs/amberformat.o MCDLformat.cpp:1320:6: warning: '/*' within block comment [-Wcomment] //***************************************************************************** ^ MCDLformat.cpp:1323:6: warning: '/*' within block comment [-Wcomment] //***************************************************************************** ^ MCDLformat.cpp:1536:24: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] chargestring="1,"+abs(netcharge); ~~~~^~~~~~~~~~~~~~~ MCDLformat.cpp:1536:24: note: use array indexing to silence this warning chargestring="1,"+abs(netcharge); ^ & [ ] MCDLformat.cpp:1549:25: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] radicalstring="1,"+abs(netcharge)+'*'; ~~~~^~~~~~~~~~~~~~~ MCDLformat.cpp:1549:25: note: use array indexing to silence this warning radicalstring="1,"+abs(netcharge)+'*'; ^ & [ ] In file included from adfformat.cpp:36: ../../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from adfformat.cpp:36: ../../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ mv -f .deps/APIInterface.Tpo .deps/APIInterface.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT balstformat.lo -MD -MP -MF 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-MD -MP -MF .deps/gausszmatformat.Tpo -c -o gausszmatformat.lo gausszmatformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT gausszmatformat.lo -MD -MP -MF .deps/gausszmatformat.Tpo -c gausszmatformat.cpp -fno-common -DPIC -o .libs/gausszmatformat.o mv -f .deps/fastsearchformat.Tpo .deps/fastsearchformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT gromos96format.lo -MD -MP -MF .deps/gromos96format.Tpo -c -o gromos96format.lo gromos96format.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT gromos96format.lo -MD -MP -MF .deps/gromos96format.Tpo -c gromos96format.cpp -fno-common -DPIC -o .libs/gromos96format.o In file included from gausscubeformat.cpp:29: ../../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from gausscubeformat.cpp:29: ../../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ gausscubeformat.cpp:104:17: warning: unused variable 'title' [-Wunused-variable] const char* title = pConv->GetTitle(); ^ mv -f .deps/freefracformat.Tpo .deps/freefracformat.Plo /bin/sh 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.libs/jaguarformat.o gausscubeformat.cpp:606:40: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat] snprintf(buffer, BUFF_SIZE," %5d", grids.size()); ~~~ ^~~~~~~~~~~~ %5lu mv -f .deps/gromos96format.Tpo .deps/gromos96format.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mdlformat.lo -MD -MP -MF .deps/mdlformat.Tpo -c -o mdlformat.lo mdlformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mdlformat.lo -MD -MP -MF .deps/mdlformat.Tpo -c mdlformat.cpp -fno-common -DPIC -o .libs/mdlformat.o mv -f .deps/gaussformat.Tpo .deps/gaussformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT alias.lo -MD -MP -MF .deps/alias.Tpo 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-MT mmcifformat.lo -MD -MP -MF .deps/mmcifformat.Tpo -c mmcifformat.cpp -fno-common -DPIC -o .libs/mmcifformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mmodformat.lo -MD -MP -MF .deps/mmodformat.Tpo -c mmodformat.cpp -fno-common -DPIC -o .libs/mmodformat.o 4 warnings generated. mv -f .deps/gausscubeformat.Tpo .deps/gausscubeformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mpdformat.lo -MD -MP -MF .deps/mpdformat.Tpo -c -o mpdformat.lo mpdformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mpdformat.lo -MD -MP -MF .deps/mpdformat.Tpo -c mpdformat.cpp -fno-common -DPIC -o .libs/mpdformat.o mv -f .deps/hinformat.Tpo .deps/hinformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mol2format.lo -MD -MP -MF .deps/mol2format.Tpo -c -o mol2format.lo mol2format.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mol2format.lo -MD -MP -MF .deps/mol2format.Tpo -c mol2format.cpp -fno-common -DPIC -o .libs/mol2format.o mv -f .deps/jaguarformat.Tpo .deps/jaguarformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT moldenformat.lo -MD -MP -MF .deps/moldenformat.Tpo -c -o moldenformat.lo moldenformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT moldenformat.lo -MD -MP -MF .deps/moldenformat.Tpo -c moldenformat.cpp -fno-common -DPIC -o .libs/moldenformat.o mv -f .deps/gamessformat.Tpo .deps/gamessformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT molreport.lo -MD -MP -MF .deps/molreport.Tpo -c -o molreport.lo molreport.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT molreport.lo -MD -MP -MF .deps/molreport.Tpo -c molreport.cpp -fno-common -DPIC -o .libs/molreport.o mmodformat.cpp:87:14: warning: variable 'natoms' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if ( !vs.empty() && vs.size() > 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmodformat.cpp:90:13: note: uninitialized use occurs here if (natoms == 0) ^~~~~~ mmodformat.cpp:87:9: note: remove the 'if' if its condition is always true if ( !vs.empty() && vs.size() > 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmodformat.cpp:87:14: warning: variable 'natoms' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] if ( !vs.empty() && vs.size() > 0) ^~~~~~~~~~~ mmodformat.cpp:90:13: note: uninitialized use occurs here if (natoms == 0) ^~~~~~ mmodformat.cpp:87:14: note: remove the '&&' if its condition is always true if ( !vs.empty() && vs.size() > 0) ^~~~~~~~~~~~~~~ mmodformat.cpp:79:15: note: initialize the variable 'natoms' to silence this warning int natoms; ^ = 0 mmodformat.cpp:220:15: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if (nbr->IsNitrogen()) ^ mv -f .deps/alias.Tpo .deps/alias.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mopacformat.lo -MD -MP -MF .deps/mopacformat.Tpo -c -o mopacformat.lo mopacformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mopacformat.lo -MD -MP -MF .deps/mopacformat.Tpo -c mopacformat.cpp -fno-common -DPIC -o .libs/mopacformat.o mv -f .deps/mpdformat.Tpo .deps/mpdformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT molproformat.lo -MD -MP -MF .deps/molproformat.Tpo -c -o molproformat.lo molproformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT molproformat.lo -MD -MP -MF .deps/molproformat.Tpo -c molproformat.cpp -fno-common -DPIC -o .libs/molproformat.o mmcifformat.cpp:45:8: warning: expression result unused [-Wunused-value] "Read Options e.g. -as\n" ^~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. mv -f .deps/mmodformat.Tpo .deps/mmodformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT msiformat.lo -MD -MP -MF .deps/msiformat.Tpo -c -o msiformat.lo msiformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT msiformat.lo -MD -MP -MF .deps/msiformat.Tpo -c msiformat.cpp -fno-common -DPIC -o .libs/msiformat.o mv -f .deps/molreport.Tpo .deps/molreport.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT msmsformat.lo -MD -MP -MF .deps/msmsformat.Tpo -c -o msmsformat.lo msmsformat.cpp mv -f .deps/mdlformat.Tpo .deps/mdlformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mpqcformat.lo -MD -MP -MF .deps/mpqcformat.Tpo -c -o mpqcformat.lo mpqcformat.cpp mv -f .deps/mol2format.Tpo .deps/mol2format.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT nwchemformat.lo -MD -MP -MF .deps/nwchemformat.Tpo -c -o nwchemformat.lo nwchemformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT msmsformat.lo -MD -MP -MF .deps/msmsformat.Tpo -c msmsformat.cpp -fno-common -DPIC -o .libs/msmsformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT mpqcformat.lo -MD -MP -MF .deps/mpqcformat.Tpo -c mpqcformat.cpp -fno-common -DPIC -o .libs/mpqcformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT nwchemformat.lo -MD -MP -MF .deps/nwchemformat.Tpo -c nwchemformat.cpp -fno-common -DPIC -o .libs/nwchemformat.o mv -f .deps/moldenformat.Tpo .deps/moldenformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT outformat.lo -MD -MP -MF .deps/outformat.Tpo -c -o outformat.lo outformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT outformat.lo -MD -MP -MF .deps/outformat.Tpo -c outformat.cpp -fno-common -DPIC -o .libs/outformat.o msiformat.cpp:71:17: warning: unused variable 'title' [-Wunused-variable] const char* title = pConv->GetTitle(); ^ 1 warning generated. mv -f .deps/mmcifformat.Tpo .deps/mmcifformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pcmodelformat.lo -MD -MP -MF .deps/pcmodelformat.Tpo -c -o pcmodelformat.lo pcmodelformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pcmodelformat.lo -MD -MP -MF .deps/pcmodelformat.Tpo -c pcmodelformat.cpp -fno-common -DPIC -o .libs/pcmodelformat.o mv -f .deps/msmsformat.Tpo .deps/msmsformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pdbformat.lo -MD -MP -MF .deps/pdbformat.Tpo -c -o pdbformat.lo pdbformat.cpp mv -f .deps/mpqcformat.Tpo .deps/mpqcformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT povrayformat.lo -MD -MP -MF .deps/povrayformat.Tpo -c -o povrayformat.lo povrayformat.cpp 1 warning generated. mv -f .deps/msiformat.Tpo .deps/msiformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pqrformat.lo -MD -MP -MF .deps/pqrformat.Tpo -c -o pqrformat.lo pqrformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pdbformat.lo -MD -MP -MF .deps/pdbformat.Tpo -c pdbformat.cpp -fno-common -DPIC -o .libs/pdbformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT povrayformat.lo -MD -MP -MF .deps/povrayformat.Tpo -c povrayformat.cpp -fno-common -DPIC -o .libs/povrayformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pqrformat.lo -MD -MP -MF .deps/pqrformat.Tpo -c pqrformat.cpp -fno-common -DPIC -o .libs/pqrformat.o mv -f .deps/molproformat.Tpo .deps/molproformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT opendxformat.lo -MD -MP -MF .deps/opendxformat.Tpo -c -o opendxformat.lo opendxformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT opendxformat.lo -MD -MP -MF .deps/opendxformat.Tpo -c opendxformat.cpp -fno-common -DPIC -o .libs/opendxformat.o mv -f .deps/nwchemformat.Tpo .deps/nwchemformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT qchemformat.lo -MD -MP -MF .deps/qchemformat.Tpo -c -o qchemformat.lo qchemformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT qchemformat.lo -MD -MP -MF .deps/qchemformat.Tpo -c qchemformat.cpp -fno-common -DPIC -o .libs/qchemformat.o mv -f .deps/mopacformat.Tpo .deps/mopacformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT reportformat.lo -MD -MP -MF .deps/reportformat.Tpo -c -o reportformat.lo reportformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT reportformat.lo -MD -MP -MF .deps/reportformat.Tpo -c reportformat.cpp -fno-common -DPIC -o .libs/reportformat.o pqrformat.cpp:196:13: warning: unused variable 'atom' [-Wunused-variable] OBAtom *atom = mol.GetAtom(mol.NumAtoms()); ^ pqrformat.cpp:211:13: warning: unused variable 'atom' [-Wunused-variable] OBAtom *atom = mol.GetAtom(mol.NumAtoms()); ^ pqrformat.cpp:277:60: warning: '&&' within '||' [-Wlogical-op-parentheses] strncasecmp(type.c_str(), "Zn", 2) != 0 && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ pqrformat.cpp:277:60: note: place parentheses around the '&&' expression to silence this warning strncasecmp(type.c_str(), "Zn", 2) != 0 && ^ mv -f .deps/outformat.Tpo .deps/outformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT shelxformat.lo -MD -MP -MF .deps/shelxformat.Tpo -c -o shelxformat.lo shelxformat.cpp In file included from opendxformat.cpp:25: ../../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from opendxformat.cpp:25: ../../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT shelxformat.lo -MD -MP -MF .deps/shelxformat.Tpo -c shelxformat.cpp -fno-common -DPIC -o .libs/shelxformat.o mv -f .deps/pcmodelformat.Tpo .deps/pcmodelformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT smilesformat.lo -MD -MP -MF .deps/smilesformat.Tpo -c -o smilesformat.lo smilesformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT smilesformat.lo -MD -MP -MF .deps/smilesformat.Tpo -c smilesformat.cpp -fno-common -DPIC -o .libs/smilesformat.o pdbformat.cpp:814:60: warning: '&&' within '||' [-Wlogical-op-parentheses] strncasecmp(type.c_str(), "Zn", 2) != 0 && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ pdbformat.cpp:814:60: note: place parentheses around the '&&' expression to silence this warning strncasecmp(type.c_str(), "Zn", 2) != 0 && ^ 2 warnings generated. mv -f .deps/opendxformat.Tpo .deps/opendxformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT thermoformat.lo -MD -MP -MF .deps/thermoformat.Tpo -c -o thermoformat.lo thermoformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT thermoformat.lo -MD -MP -MF .deps/thermoformat.Tpo -c thermoformat.cpp -fno-common -DPIC -o .libs/thermoformat.o mv -f .deps/povrayformat.Tpo .deps/povrayformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT tinkerformat.lo -MD -MP -MF .deps/tinkerformat.Tpo -c -o tinkerformat.lo tinkerformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT tinkerformat.lo -MD -MP -MF .deps/tinkerformat.Tpo -c tinkerformat.cpp -fno-common -DPIC -o .libs/tinkerformat.o 3 warnings generated. mv -f .deps/pqrformat.Tpo .deps/pqrformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT titleformat.lo -MD -MP -MF .deps/titleformat.Tpo -c -o titleformat.lo titleformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT titleformat.lo -MD -MP -MF .deps/titleformat.Tpo -c titleformat.cpp -fno-common -DPIC -o .libs/titleformat.o mv -f .deps/qchemformat.Tpo .deps/qchemformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT turbomoleformat.lo -MD -MP -MF .deps/turbomoleformat.Tpo -c -o turbomoleformat.lo turbomoleformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT turbomoleformat.lo -MD -MP -MF .deps/turbomoleformat.Tpo -c turbomoleformat.cpp -fno-common -DPIC -o .libs/turbomoleformat.o thermoformat.cpp:78:48: warning: '&&' within '||' [-Wlogical-op-parentheses] if(!ifs.getline(ln,BUFF_SIZE) || stopOnEnd && !strncasecmp(ln,"END",3)) ~~ ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ thermoformat.cpp:78:48: note: place parentheses around the '&&' expression to silence this warning if(!ifs.getline(ln,BUFF_SIZE) || stopOnEnd && !strncasecmp(ln,"END",3)) ^ ( ) mv -f .deps/shelxformat.Tpo .deps/shelxformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT unichemformat.lo -MD -MP -MF .deps/unichemformat.Tpo -c -o unichemformat.lo unichemformat.cpp 1 warning generated. mv -f .deps/pdbformat.Tpo .deps/pdbformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT vaspformat.lo -MD -MP -MF .deps/vaspformat.Tpo -c -o vaspformat.lo vaspformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT unichemformat.lo -MD -MP -MF .deps/unichemformat.Tpo -c unichemformat.cpp -fno-common -DPIC -o .libs/unichemformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT vaspformat.lo -MD -MP -MF .deps/vaspformat.Tpo -c vaspformat.cpp -fno-common -DPIC -o .libs/vaspformat.o mv -f .deps/reportformat.Tpo .deps/reportformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT viewmolformat.lo -MD -MP -MF .deps/viewmolformat.Tpo -c -o viewmolformat.lo viewmolformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT viewmolformat.lo -MD -MP -MF .deps/viewmolformat.Tpo -c viewmolformat.cpp -fno-common -DPIC -o .libs/viewmolformat.o smilesformat.cpp:1176:19: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ smilesformat.cpp:3963:11: warning: unused variable 'bo' [-Wunused-variable] int bo = (bond1->IsAromatic())? 1 : bond1->GetBO(); // CJ: why was this line added? bo is never used? ^ mv -f .deps/tinkerformat.Tpo .deps/tinkerformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT xedformat.lo -MD -MP -MF .deps/xedformat.Tpo -c -o xedformat.lo xedformat.cpp smilesformat.cpp:4386:10: warning: unused variable 'is_modified' [-Wunused-variable] bool is_modified = false; ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT xedformat.lo -MD -MP -MF .deps/xedformat.Tpo -c xedformat.cpp -fno-common -DPIC -o .libs/xedformat.o 1 warning generated. mv -f .deps/thermoformat.Tpo .deps/thermoformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT xtcformat.lo -MD -MP -MF .deps/xtcformat.Tpo -c -o xtcformat.lo xtcformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT xtcformat.lo -MD -MP -MF .deps/xtcformat.Tpo -c xtcformat.cpp -fno-common -DPIC -o .libs/xtcformat.o smilesformat.cpp:2676:15: warning: unused function 'IsCisOrTransH' [-Wunused-function] static bool IsCisOrTransH(OBAtom *atom) ^ mv -f .deps/titleformat.Tpo .deps/titleformat.Plo /bin/sh ../../libtool 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NULL xtcformat.cpp:675:26: warning: variable 'oldsize' is uninitialized when used here [-Wuninitialized] } else if (*size > oldsize) { ^~~~~~~ xtcformat.cpp:619:16: note: initialize the variable 'oldsize' to silence this warning int oldsize; ^ = 0 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT yasaraformat.lo -MD -MP -MF .deps/yasaraformat.Tpo -c yasaraformat.cpp -fno-common -DPIC -o .libs/yasaraformat.o mv -f .deps/viewmolformat.Tpo .deps/viewmolformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT zindoformat.lo -MD -MP -MF .deps/zindoformat.Tpo -c -o zindoformat.lo zindoformat.cpp mv -f .deps/unichemformat.Tpo .deps/unichemformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 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-I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT getinchi.lo -MD -MP -MF .deps/getinchi.Tpo -c getinchi.cpp -fno-common -DPIC -o .libs/getinchi.o mv -f .deps/vaspformat.Tpo .deps/vaspformat.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pngformat.lo -MD -MP -MF .deps/pngformat.Tpo -c -o pngformat.lo pngformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT pngformat.lo -MD -MP -MF .deps/pngformat.Tpo -c pngformat.cpp -fno-common -DPIC -o .libs/pngformat.o mv -f .deps/getinchi.Tpo .deps/getinchi.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT gamessukformat.lo -MD -MP -MF .deps/gamessukformat.Tpo -c -o gamessukformat.lo gamessukformat.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -I../../include -I../../data -I../../include -I/sw/include -Wall -g -O2 -MT gamessukformat.lo -MD -MP -MF .deps/gamessukformat.Tpo -c gamessukformat.cpp -fno-common -DPIC -o .libs/gamessukformat.o 3 warnings generated. mv -f .deps/xtcformat.Tpo .deps/xtcformat.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined ../libopenbabel.la -L/sw/lib -o APIInterface.la -rpath /sw/lib/openbabel/2.2.3 APIInterface.lo -lz -lm inchiformat.cpp:115:50: warning: while loop has empty body [-Wempty-body] while(p1!=s1.end() && isdigit(*p1++)); --p1; ^ inchiformat.cpp:115:50: note: put the semicolon on a separate line to silence this warning inchiformat.cpp:120:50: warning: while loop has empty body [-Wempty-body] while(p2!=s2.end() && isdigit(*p2++)); --p2; ^ inchiformat.cpp:120:50: note: put the semicolon on a separate line to silence this warning mv -f .deps/pngformat.Tpo 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-bundle .libs/cccformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: ( cd ".libs" && rm -f "cacaoformat.la" && ln -s "../cacaoformat.la" "cacaoformat.la" ) libtool: link: ( cd ".libs" && rm -f "cacheformat.la" && ln -s "../cacheformat.la" "cacheformat.la" ) /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined ../libopenbabel.la -L/sw/lib -o chemdrawctformat.la -rpath /sw/lib/openbabel/2.2.3 chemdrawct.lo -lz -lm /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined ../libopenbabel.la -L/sw/lib -o chemtoolformat.la -rpath /sw/lib/openbabel/2.2.3 chemtoolformat.lo -lz -lm libtool: link: ( cd ".libs" && rm -f "carformat.la" && ln -s "../carformat.la" "carformat.la" ) libtool: link: ( cd ".libs" && rm -f "cccformat.la" && ln -s "../cccformat.la" "cccformat.la" ) /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined ../libopenbabel.la 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inchiformat.lo getinchi.lo -lstdinchi -lz -lm libtool: link: g++ -o .libs/viewmolformat.so -bundle .libs/viewmolformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: g++ -o .libs/xedformat.so -bundle .libs/xedformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: ( cd ".libs" && rm -f "vaspformat.la" && ln -s "../vaspformat.la" "vaspformat.la" ) /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined ../libopenbabel.la -L/sw/lib -o pngformat.la -rpath /sw/lib/openbabel/2.2.3 pngformat.lo -lz -lz -lm libtool: link: ( cd ".libs" && rm -f "viewmolformat.la" && ln -s "../viewmolformat.la" "viewmolformat.la" ) /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -module -avoid-version -no-undefined ../libopenbabel.la -L/sw/lib -o gamessukformat.la -rpath /sw/lib/openbabel/2.2.3 gamessukformat.lo -lz -lm libtool: link: g++ -o .libs/xtcformat.so -bundle .libs/xtcformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: ( cd ".libs" && rm -f "xedformat.la" && ln -s "../xedformat.la" "xedformat.la" ) libtool: link: g++ -o .libs/yasaraformat.so -bundle .libs/yasaraformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: g++ -o .libs/xyzformat.so -bundle .libs/xyzformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: g++ -o .libs/zindoformat.so -bundle .libs/zindoformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: ( cd ".libs" && rm -f "xtcformat.la" && ln -s "../xtcformat.la" "xtcformat.la" ) libtool: link: ( cd ".libs" && rm -f "yasaraformat.la" && ln -s "../yasaraformat.la" "yasaraformat.la" ) libtool: link: ( cd ".libs" && rm -f "xyzformat.la" && ln -s "../xyzformat.la" "xyzformat.la" ) libtool: link: ( cd ".libs" && rm -f "zindoformat.la" && ln -s "../zindoformat.la" "zindoformat.la" ) libtool: link: g++ -o .libs/inchiformat.so -bundle .libs/inchiformat.o .libs/getinchi.o ../.libs/libopenbabel.dylib -L/sw/lib -lstdinchi -lz -lm -O2 libtool: link: g++ -o .libs/pngformat.so -bundle .libs/pngformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: g++ -o .libs/gamessukformat.so -bundle .libs/gamessukformat.o ../.libs/libopenbabel.dylib -L/sw/lib -lz -lm -O2 libtool: link: ( cd ".libs" && rm -f "inchiformat.la" && ln -s "../inchiformat.la" "inchiformat.la" ) libtool: link: ( cd ".libs" && rm -f "pngformat.la" && ln -s "../pngformat.la" "pngformat.la" ) libtool: link: ( cd ".libs" && rm -f "gamessukformat.la" && ln -s "../gamessukformat.la" "gamessukformat.la" ) Making all in test Making all in cmltest make[2]: Nothing to be done for `all'. g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -DTESTDATADIR="\"../test/files/\"" -I/sw/include -Wall -g -O2 -MT roundtrip.o -MD -MP -MF .deps/roundtrip.Tpo -c -o roundtrip.o roundtrip.cpp mv -f .deps/roundtrip.Tpo .deps/roundtrip.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o roundtrip roundtrip.o ../src/libopenbabel.la -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/roundtrip roundtrip.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm Making all in tools g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT babel.o -MD -MP -MF .deps/babel.Tpo -c -o babel.o babel.cpp g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obchiral.o -MD -MP -MF .deps/obchiral.Tpo -c -o obchiral.o obchiral.cpp g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obconformer.o -MD -MP -MF .deps/obconformer.Tpo -c -o obconformer.o obconformer.cpp g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obenergy.o -MD -MP -MF .deps/obenergy.Tpo -c -o obenergy.o obenergy.cpp g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obfit.o -MD -MP -MF .deps/obfit.Tpo -c -o obfit.o obfit.cpp g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obgen.o -MD -MP -MF .deps/obgen.Tpo -c -o obgen.o obgen.cpp g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obgrep.o -MD -MP -MF .deps/obgrep.Tpo -c -o obgrep.o obgrep.cpp g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obminimize.o -MD -MP -MF .deps/obminimize.Tpo -c -o obminimize.o obminimize.cpp In file included from obgen.cpp:30: In file included from ../include/openbabel/forcefield.h:32: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from obminimize.cpp:29: In file included from ../include/openbabel/forcefield.h:32: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from obgen.cpp:30: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from obgen.cpp:30: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ In file included from obenergy.cpp:28: In file included from ../include/openbabel/forcefield.h:32: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from obminimize.cpp:29: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from obminimize.cpp:29: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ In file included from obenergy.cpp:28: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from obenergy.cpp:28: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ In file included from obconformer.cpp:32: In file included from ../include/openbabel/forcefield.h:32: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from obconformer.cpp:32: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from obconformer.cpp:32: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ mv -f .deps/babel.Tpo .deps/babel.Po g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obprobe.o -MD -MP -MF .deps/obprobe.Tpo -c -o obprobe.o obprobe.cpp mv -f .deps/obchiral.Tpo .deps/obchiral.Po g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obprop.o -MD -MP -MF .deps/obprop.Tpo -c -o obprop.o obprop.cpp 3 warnings generated. mv -f .deps/obgen.Tpo .deps/obgen.Po g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obrotamer.o -MD -MP -MF .deps/obrotamer.Tpo -c -o obrotamer.o obrotamer.cpp mv -f .deps/obgrep.Tpo .deps/obgrep.Po g++ -DHAVE_CONFIG_H -I. -I../src -I../include -I../include -I/sw/include -Wall -g -O2 -MT obrotate.o -MD -MP -MF .deps/obrotate.Tpo -c -o obrotate.o obrotate.cpp 3 warnings generated. mv -f .deps/obconformer.Tpo .deps/obconformer.Po 3 warnings generated. /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o babel babel.o ../src/libopenbabel.la -lz -lm mv -f .deps/obenergy.Tpo .deps/obenergy.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obchiral obchiral.o ../src/libopenbabel.la -lz -lm 3 warnings generated. mv -f .deps/obminimize.Tpo .deps/obminimize.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obconformer obconformer.o ../src/libopenbabel.la -lz -lm mv -f .deps/obfit.Tpo .deps/obfit.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obenergy obenergy.o ../src/libopenbabel.la -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obchiral obchiral.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/babel babel.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obconformer obconformer.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obenergy obenergy.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obfit obfit.o ../src/libopenbabel.la -lz -lm /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obgen obgen.o ../src/libopenbabel.la -lz -lm /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obgrep obgrep.o ../src/libopenbabel.la -lz -lm /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obminimize obminimize.o ../src/libopenbabel.la -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obgrep obgrep.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obminimize obminimize.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obgen obgen.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obfit obfit.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm In file included from obprobe.cpp:31: In file included from ../include/openbabel/forcefield.h:32: ../include/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual] void Init(OBMol &box,double spacing, double pad=0.0); ^ ../include/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3) virtual void Init(OBMol &box); ^ In file included from obprobe.cpp:31: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue(int i, int j, int k) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3) virtual const std::string &GetValue() const ^ In file included from obprobe.cpp:31: In file included from ../include/openbabel/forcefield.h:33: ../include/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual] double GetValue (vector3 pos) const; ^ ../include/openbabel/base.h:206:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1) virtual const std::string &GetValue() const ^ obrotamer.cpp:76:8: warning: unused variable 'rotorKey' [-Wunused-variable] int *rotorKey = NULL; ^ 3 warnings generated. mv -f .deps/obprobe.Tpo .deps/obprobe.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obprobe obprobe.o ../src/libopenbabel.la -lz -lm mv -f .deps/obprop.Tpo .deps/obprop.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obprop obprop.o ../src/libopenbabel.la -lz -lm 1 warning generated. libtool: link: g++ -Wall -g -O2 -o .libs/obprobe obprobe.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm mv -f .deps/obrotamer.Tpo .deps/obrotamer.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obrotamer obrotamer.o ../src/libopenbabel.la -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obprop obprop.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obrotamer obrotamer.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm mv -f .deps/obrotate.Tpo .deps/obrotate.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -L/sw/lib -o obrotate obrotate.o ../src/libopenbabel.la -lz -lm libtool: link: g++ -Wall -g -O2 -o .libs/obrotate obrotate.o -L/sw/lib ../src/.libs/libopenbabel.dylib -lz -lm Making all in doc make[1]: Nothing to be done for `all'. Making all in include Making all in openbabel Making all in math make[3]: Nothing to be done for `all'. make[3]: Nothing to be done for `all-am'. make[2]: Nothing to be done for `all-am'. Making all in scripts /Applications/Xcode.app/Contents/Developer/usr/bin/make all-am make[2]: Nothing to be done for `all-am'. make[1]: Nothing to be done for `all-am'. /bin/rm -rf /sw/build.build/root-openbabel-2.2.3-11 /bin/mkdir -p /sw/build.build/root-openbabel-2.2.3-11/sw /bin/mkdir -p /sw/build.build/root-openbabel-2.2.3-11/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-openbabel-2.2.3-11 sudo -u fink-bld [ENV] sh -c /tmp/fink.5JBi2 make install DESTDIR=/sw/build.build/root-openbabel-2.2.3-11 Making install in data /Applications/Xcode.app/Contents/Developer/usr/bin/make install-am make[3]: Nothing to be done for `install-exec-am'. .././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/share/openbabel/2.2.3' /usr/bin/install -c -m 644 aromatic.txt bondtyp.txt isotope.txt resdata.txt atomtyp.txt element.txt isotope-small.txt phmodel.txt patterns.txt torlib.txt types.txt space-groups.txt SMARTS_InteLigand.txt fragments.txt ghemical.prm UFF.prm ringtyp.txt mmffoop.par mmffchg.par mmfftor.par mmffang.par mmffpbci.par mmffdef.par mmffvdw.par mmffstbn.par mmffbndk.par mmffprop.par mmffbond.par mmffdfsb.par mmffs_oop.par mmffs_tor.par mmff94.ff mmff94s.ff logp.txt psa.txt mr.txt plugindefines.txt MACCS.txt '/sw/build.build/root-openbabel-2.2.3-11/sw/share/openbabel/2.2.3' Making install in src /Applications/Xcode.app/Contents/Developer/usr/bin/make install-recursive Making install in math make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. Making install in fingerprints make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. Making install in forcefields make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. Making install in descriptors make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. Making install in ops make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. Making install in . .././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libopenbabel.la '/sw/build.build/root-openbabel-2.2.3-11/sw/lib' libtool: install: /usr/bin/install -c .libs/libopenbabel.3.dylib /sw/build.build/root-openbabel-2.2.3-11/sw/lib/libopenbabel.3.dylib libtool: install: (cd /sw/build.build/root-openbabel-2.2.3-11/sw/lib && { ln -s -f libopenbabel.3.dylib libopenbabel.dylib || { rm -f libopenbabel.dylib && ln -s libopenbabel.3.dylib libopenbabel.dylib; }; }) libtool: install: /usr/bin/install -c .libs/libopenbabel.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/libopenbabel.la libtool: install: warning: remember to run `libtool --finish /sw/lib' make[4]: Nothing to be done for `install-data-am'. Making install in formats /Applications/Xcode.app/Contents/Developer/usr/bin/make install-recursive Making install in xml make[6]: Nothing to be done for `install-exec-am'. ../../.././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3' /bin/sh ../../../libtool --mode=install /usr/bin/install -c pubchem.la xmlformat.la cdxmlformat.la cmlformat.la '/sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3' libtool: install: /usr/bin/install -c .libs/pubchem.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/pubchem.so libtool: install: /usr/bin/install -c .libs/pubchem.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/pubchem.la libtool: install: /usr/bin/install -c .libs/xmlformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xmlformat.so libtool: install: /usr/bin/install -c .libs/xmlformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xmlformat.la libtool: install: 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/sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/pqrformat.la libtool: install: /usr/bin/install -c .libs/opendxformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/opendxformat.so libtool: install: /usr/bin/install -c .libs/opendxformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/opendxformat.la libtool: install: /usr/bin/install -c .libs/qchemformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/qchemformat.so libtool: install: /usr/bin/install -c .libs/qchemformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/qchemformat.la libtool: install: /usr/bin/install -c .libs/reportformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/reportformat.so libtool: install: /usr/bin/install -c .libs/reportformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/reportformat.la libtool: install: /usr/bin/install -c .libs/shelxformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/shelxformat.so libtool: install: /usr/bin/install -c .libs/shelxformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/shelxformat.la libtool: install: /usr/bin/install -c .libs/smilesformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/smilesformat.so libtool: install: /usr/bin/install -c .libs/smilesformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/smilesformat.la libtool: install: /usr/bin/install -c .libs/thermoformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/thermoformat.so libtool: install: /usr/bin/install -c .libs/thermoformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/thermoformat.la libtool: install: /usr/bin/install -c .libs/tinkerformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/tinkerformat.so libtool: install: /usr/bin/install -c .libs/tinkerformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/tinkerformat.la libtool: install: /usr/bin/install -c .libs/titleformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/titleformat.so libtool: install: /usr/bin/install -c .libs/titleformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/titleformat.la libtool: install: /usr/bin/install -c .libs/turbomoleformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/turbomoleformat.so libtool: install: /usr/bin/install -c .libs/turbomoleformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/turbomoleformat.la libtool: install: /usr/bin/install -c .libs/unichemformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/unichemformat.so libtool: install: /usr/bin/install -c .libs/unichemformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/unichemformat.la libtool: install: /usr/bin/install -c .libs/vaspformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/vaspformat.so libtool: install: /usr/bin/install -c .libs/vaspformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/vaspformat.la libtool: install: /usr/bin/install -c .libs/viewmolformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/viewmolformat.so libtool: install: /usr/bin/install -c .libs/viewmolformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/viewmolformat.la libtool: install: /usr/bin/install -c .libs/xedformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xedformat.so libtool: install: /usr/bin/install -c .libs/xedformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xedformat.la libtool: install: /usr/bin/install -c .libs/xtcformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xtcformat.so libtool: install: /usr/bin/install -c .libs/xtcformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xtcformat.la libtool: install: /usr/bin/install -c .libs/xyzformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xyzformat.so libtool: install: /usr/bin/install -c .libs/xyzformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/xyzformat.la libtool: install: /usr/bin/install -c .libs/yasaraformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/yasaraformat.so libtool: install: /usr/bin/install -c .libs/yasaraformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/yasaraformat.la libtool: install: /usr/bin/install -c .libs/zindoformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/zindoformat.so libtool: install: /usr/bin/install -c .libs/zindoformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/zindoformat.la libtool: install: /usr/bin/install -c .libs/inchiformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/inchiformat.so libtool: install: /usr/bin/install -c .libs/inchiformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/inchiformat.la libtool: install: /usr/bin/install -c .libs/pngformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/pngformat.so libtool: install: /usr/bin/install -c .libs/pngformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/pngformat.la libtool: install: /usr/bin/install -c .libs/gamessukformat.so /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/gamessukformat.so libtool: install: /usr/bin/install -c .libs/gamessukformat.lai /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel/2.2.3/gamessukformat.la libtool: install: warning: remember to run `libtool --finish /sw/lib/openbabel/2.2.3' /Applications/Xcode.app/Contents/Developer/usr/bin/make install-data-hook make[7]: Nothing to be done for `install-data-hook'. Making install in test Making install in cmltest make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. .././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c roundtrip '/sw/build.build/root-openbabel-2.2.3-11/sw/bin' libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/roundtrip /sw/build.build/root-openbabel-2.2.3-11/sw/bin/roundtrip make[3]: Nothing to be done for `install-data-am'. Making install in tools .././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c babel obchiral obconformer obenergy obfit obgen obgrep obminimize obprobe obprop obrotamer obrotate '/sw/build.build/root-openbabel-2.2.3-11/sw/bin' libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/babel /sw/build.build/root-openbabel-2.2.3-11/sw/bin/babel libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obchiral /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obchiral libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obconformer /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obconformer libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obenergy /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obenergy libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obfit /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obfit libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obgen /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obgen libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obgrep /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obgrep libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obminimize /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obminimize libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obprobe /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obprobe libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obprop /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obprop libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obrotamer /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obrotamer libtool: install: warning: `../src/libopenbabel.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/obrotate /sw/build.build/root-openbabel-2.2.3-11/sw/bin/obrotate make[2]: Nothing to be done for `install-data-am'. Making install in doc make[2]: Nothing to be done for `install-exec-am'. .././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/share/man/man1' /usr/bin/install -c -m 644 babel.1 obchiral.1 obfit.1 obgrep.1 obrotate.1 obprop.1 obminimize.1 obenergy.1 obrotamer.1 obprobe.1 obgen.1 obconformer.1 roundtrip.1 '/sw/build.build/root-openbabel-2.2.3-11/sw/share/man/man1' Making install in include Making install in openbabel Making install in math make[4]: Nothing to be done for `install-exec-am'. ../../.././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/include/openbabel-2.0/openbabel/math' /usr/bin/install -c -m 644 matrix3x3.h vector3.h transform3d.h spacegroup.h '/sw/build.build/root-openbabel-2.2.3-11/sw/include/openbabel-2.0/openbabel/math' make[4]: Nothing to be done for `install-exec-am'. ../.././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/include/openbabel-2.0/openbabel' /usr/bin/install -c -m 644 alias.h atom.h atomclass.h babelconfig.h base.h bitvec.h bond.h bondtyper.h builder.h canon.h chains.h chiral.h data.h descriptor.h dlhandler.h fingerprint.h forcefield.h format.h generic.h grid.h griddata.h groupcontrib.h internalcoord.h kinetics.h locale.h lineend.h matrix.h mol.h molchrg.h obconversion.h oberror.h obiter.h obmolecformat.h obutil.h op.h optransform.h parsmart.h patty.h phmodel.h plugin.h '/sw/build.build/root-openbabel-2.2.3-11/sw/include/openbabel-2.0/openbabel' /usr/bin/install -c -m 644 pointgroup.h rand.h reaction.h residue.h ring.h rotamer.h rotor.h tokenst.h typer.h xml.h '/sw/build.build/root-openbabel-2.2.3-11/sw/include/openbabel-2.0/openbabel' make[3]: Nothing to be done for `install-exec-am'. .././install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/include/openbabel-2.0/openbabel' /usr/bin/install -c -m 644 chemdrawcdx.h '/sw/build.build/root-openbabel-2.2.3-11/sw/include/openbabel-2.0/openbabel' Making install in scripts /Applications/Xcode.app/Contents/Developer/usr/bin/make install-am make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[2]: Nothing to be done for `install-exec-am'. ./install-sh -c -d '/sw/build.build/root-openbabel-2.2.3-11/sw/lib/pkgconfig' /usr/bin/install -c -m 644 openbabel-2.0.pc '/sw/build.build/root-openbabel-2.2.3-11/sw/lib/pkgconfig' sudo -u fink-bld [ENV] sh -c /tmp/fink.6TWsl /usr/bin/install -d -m 700 /sw/build.build/root-openbabel-2.2.3-11/sw/share/doc/openbabel /bin/cp -r AUTHORS /sw/build.build/root-openbabel-2.2.3-11/sw/share/doc/openbabel/ /bin/cp -r COPYING /sw/build.build/root-openbabel-2.2.3-11/sw/share/doc/openbabel/ /bin/cp -r ChangeLog /sw/build.build/root-openbabel-2.2.3-11/sw/share/doc/openbabel/ /bin/cp -r README /sw/build.build/root-openbabel-2.2.3-11/sw/share/doc/openbabel/ /bin/cp -r THANKS /sw/build.build/root-openbabel-2.2.3-11/sw/share/doc/openbabel/ /bin/chmod -R go=u-w /sw/build.build/root-openbabel-2.2.3-11/sw/share/doc/openbabel /bin/rm -f /sw/build.build/root-openbabel-2.2.3-11/sw/info/dir /sw/build.build/root-openbabel-2.2.3-11/sw/info/dir.old /sw/build.build/root-openbabel-2.2.3-11/sw/share/info/dir /sw/build.build/root-openbabel-2.2.3-11/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11 /bin/mkdir -p /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw /bin/mkdir -p /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11 sudo -u fink-bld [ENV] sh -c /tmp/fink.tYyvz /usr/bin/install -d -m 755 /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/lib /bin/mv /sw/build.build/root-openbabel-2.2.3-11/sw/lib/libopenbabel.3*.dylib /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/lib/ /bin/mv /sw/build.build/root-openbabel-2.2.3-11/sw/lib/openbabel /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/lib/ /usr/bin/install -d -m 755 /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share /bin/mv /sw/build.build/root-openbabel-2.2.3-11/sw/share/openbabel /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/ /usr/bin/install -d -m 700 /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/doc/libopenbabel3-shlibs /bin/cp -r AUTHORS /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/doc/libopenbabel3-shlibs/ /bin/cp -r COPYING /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/doc/libopenbabel3-shlibs/ /bin/cp -r ChangeLog /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/doc/libopenbabel3-shlibs/ /bin/cp -r README /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/doc/libopenbabel3-shlibs/ /bin/cp -r THANKS /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/doc/libopenbabel3-shlibs/ /bin/chmod -R go=u-w /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/doc/libopenbabel3-shlibs /bin/rm -f /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/info/dir /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/info/dir.old /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/info/dir /sw/build.build/root-libopenbabel3-shlibs-2.2.3-11/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-libopenbabel3-dev-2.2.3-11 /bin/mkdir -p /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw /bin/mkdir -p /sw/build.build/root-libopenbabel3-dev-2.2.3-11/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-libopenbabel3-dev-2.2.3-11 sudo -u fink-bld [ENV] sh -c /tmp/fink.h_Ywg /usr/bin/install -d -m 755 /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw /bin/mv /sw/build.build/root-openbabel-2.2.3-11/sw/include /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/ /bin/mv /sw/build.build/root-openbabel-2.2.3-11/sw/lib /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/ /usr/bin/install -d -m 700 /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/doc/libopenbabel3-dev /bin/cp -r AUTHORS /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/doc/libopenbabel3-dev/ /bin/cp -r COPYING /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/doc/libopenbabel3-dev/ /bin/cp -r ChangeLog /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/doc/libopenbabel3-dev/ /bin/cp -r README /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/doc/libopenbabel3-dev/ /bin/cp -r THANKS /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/doc/libopenbabel3-dev/ /bin/chmod -R go=u-w /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/doc/libopenbabel3-dev /bin/rm -f /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/info/dir /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/info/dir.old /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/info/dir /sw/build.build/root-libopenbabel3-dev-2.2.3-11/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-openbabel-2.2.3-11 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `openbabel' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/openbabel_2.2.3-11_darwin-x86_64.deb'. Reverting ownership of install dir to root Writing control file... Creating shlibs files... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-libopenbabel3-shlibs-2.2.3-11 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `libopenbabel3-shlibs' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/libopenbabel3-shlibs_2.2.3-11_darwin-x86_64.deb'. Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-libopenbabel3-dev-2.2.3-11 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `libopenbabel3-dev' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/libopenbabel3-dev_2.2.3-11_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-openbabel-2.2.3-11 (Reading database ... 5059 files and directories currently installed.) Removing fink-buildlock-openbabel-2.2.3-11 ...