version:1 :msg:main ---> Computing dependencies for clustalx:info:main .:debug:main clustalx has no conflicts :debug:main Searching for dependency: qt4-mac :debug:main Didn't find receipt, going to depspec regex for: qt4-mac :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/aqua/qt4-mac :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main compiler clang 503.0.38 not blacklisted because it doesn't match { clang <= 318.0.61 } :debug:main adding the default universal variant :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :info:main .:debug:main Checking for conflicts against qt4-mac :debug:main Searching for dependency: qt3 :debug:main Didn't find receipt, going to depspec regex for: qt3 :debug:main Searching for dependency: qt3-mac :debug:main Didn't find receipt, going to depspec regex for: qt3-mac :debug:main Searching for dependency: zlib :debug:main Found Dependency: receipt exists for zlib :debug:main Searching for dependency: dbus :debug:main Didn't find receipt, going to depspec regex for: dbus :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/dbus :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main universal variant already exists, so not adding the default one :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Searching for dependency: openssl :debug:main Found Dependency: receipt exists for openssl :debug:main Searching for dependency: tiff :debug:main Didn't find receipt, going to depspec regex for: tiff :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/tiff :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main universal variant already exists, so not adding the default one :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Searching for dependency: libpng :debug:main Didn't find receipt, going to depspec regex for: libpng :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/libpng :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main adding the default universal variant :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Searching for dependency: libmng :debug:main Didn't find receipt, going to depspec regex for: libmng :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/libmng :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main adding the default universal variant :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Searching for dependency: jpeg :debug:main Didn't find receipt, going to depspec regex for: jpeg :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/jpeg :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main adding the default universal variant :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :info:main .:debug:main Checking for conflicts against dbus :debug:main Searching for dependency: dbus-devel :debug:main Didn't find receipt, going to depspec regex for: dbus-devel :debug:main Searching for dependency: expat :debug:main Found Dependency: receipt exists for expat :info:main .:debug:main tiff has no conflicts :debug:main Searching for dependency: xz :debug:main Didn't find receipt, going to depspec regex for: xz :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/xz :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main adding the default universal variant :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :info:main .:debug:main xz has no conflicts :debug:main Searching for dependency: libiconv :debug:main Found Dependency: receipt exists for libiconv :debug:main Searching for dependency: gettext :debug:main Found Dependency: receipt exists for gettext :info:main .:debug:main libpng has no conflicts :info:main .:debug:main libmng has no conflicts :debug:main Searching for dependency: lcms :debug:main Didn't find receipt, going to depspec regex for: lcms :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/lcms :debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386 :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf :debug:main universal variant already exists, so not adding the default one :debug:main Running callback portconfigure::add_automatic_compiler_dependencies :debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies :debug:main Running callback portbuild::add_automatic_buildsystem_dependencies :debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies :info:main .:debug:main lcms has no conflicts :info:main .:debug:main Checking for conflicts against jpeg :debug:main Searching for dependency: libjpeg-turbo :debug:main Didn't find receipt, going to depspec regex for: libjpeg-turbo :debug:main Searching for dependency: mozjpeg :debug:main Didn't find receipt, going to depspec regex for: mozjpeg :msg:main :msg:main ---> Dependencies to be installed: qt4-mac dbus jpeg libmng lcms tiff xz libpng :debug:main Starting logging for dbus :debug:clean Starting logging for jpeg :debug:clean Starting logging for xz :debug:clean Starting logging for tiff :debug:clean Starting logging for lcms :debug:clean Starting logging for libmng :debug:clean Starting logging for libpng :debug:clean Starting logging for qt4-mac :debug:main Executing org.macports.main (clustalx) :debug:main changing euid/egid - current euid: 0 - current egid: 0 :debug:main egid changed to: 501 :debug:main euid changed to: 502 :debug:archivefetch archivefetch phase started at Wed Apr 9 14:06:41 CDT 2014 :msg:archivefetch ---> Fetching archive for clustalx :debug:archivefetch Executing org.macports.archivefetch (clustalx) :debug:archivefetch euid/egid changed to: 0/0 :debug:archivefetch chowned /opt/local/var/macports/incoming to macports :debug:archivefetch euid/egid changed to: 502/501 :info:archivefetch ---> clustalx-2.1_0.darwin_13.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified :msg:archivefetch ---> Attempting to fetch clustalx-2.1_0.darwin_13.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/clustalx :debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found :msg:archivefetch ---> Attempting to fetch clustalx-2.1_0.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/clustalx :debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found :msg:archivefetch ---> Attempting to fetch clustalx-2.1_0.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/clustalx :debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found :debug:archivefetch Privilege de-escalation not attempted as not running as root. :debug:fetch fetch phase started at Wed Apr 9 14:06:42 CDT 2014 :notice:fetch ---> Fetching distfiles for clustalx :debug:fetch Can't run fetch on this port without elevated privileges. Escalating privileges back to root. :debug:fetch euid changed to: 0. egid changed to: 0. :debug:fetch changing euid/egid - current euid: 0 - current egid: 0 :debug:fetch egid changed to: 501 :debug:fetch euid changed to: 502 :debug:fetch Executing org.macports.fetch (clustalx) :info:fetch ---> clustalx-2.1.tar.gz doesn't seem to exist in /opt/local/var/macports/distfiles/clustalx :notice:fetch ---> Attempting to fetch clustalx-2.1.tar.gz from http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/clustalx :debug:fetch Privilege de-escalation not attempted as not running as root. :debug:checksum checksum phase started at Wed Apr 9 14:06:45 CDT 2014 :notice:checksum ---> Verifying checksums for clustalx :debug:checksum Executing org.macports.checksum (clustalx) :info:checksum ---> Checksumming clustalx-2.1.tar.gz :debug:checksum Correct (rmd160) checksum for clustalx-2.1.tar.gz :debug:checksum Correct (sha256) checksum for clustalx-2.1.tar.gz :debug:checksum Privilege de-escalation not attempted as not running as root. :debug:extract extract phase started at Wed Apr 9 14:06:45 CDT 2014 :notice:extract ---> Extracting clustalx :debug:extract Executing org.macports.extract (clustalx) :info:extract ---> Extracting clustalx-2.1.tar.gz :debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/clustalx/clustalx-2.1.tar.gz' :debug:extract Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9' :debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/clustalx/clustalx-2.1.tar.gz' | /usr/bin/tar -xf -' :debug:extract Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/clustalx/clustalx-2.1.tar.gz' | /usr/bin/tar -xf - :debug:extract euid/egid changed to: 0/0 :debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work to macports :debug:extract euid/egid changed to: 502/501 :debug:extract Privilege de-escalation not attempted as not running as root. :debug:patch patch phase started at Wed Apr 9 14:06:45 CDT 2014 :debug:patch Executing org.macports.patch (clustalx) :debug:patch Privilege de-escalation not attempted as not running as root. :debug:configure configure phase started at Wed Apr 9 14:06:45 CDT 2014 :notice:configure ---> Configuring clustalx :debug:configure Using compiler 'Xcode Clang' :debug:configure Executing org.macports.configure (clustalx) :debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -Os -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -Os -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.9' CXX='/usr/bin/clang++' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -Os -m64' LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names -arch x86_64' FCFLAGS='-pipe -Os -m64' OBJC='/usr/bin/clang' OBJCXX='/usr/bin/clang++' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -Os -arch x86_64' OBJCXXFLAGS='-pipe -Os -arch x86_64' FFLAGS='-pipe -Os -m64' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang' :debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/clustalx-2.1" && /opt/local/bin/qmake PREFIX=/opt/local' :debug:configure Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/clustalx-2.1" && /opt/local/bin/qmake PREFIX=/opt/local :info:configure Project MESSAGE: qtAddLibrary: found framework QtXml in directory /opt/local/Library/Frameworks :info:configure Project MESSAGE: qtAddLibrary: found framework QtGui in directory /opt/local/Library/Frameworks :info:configure Project MESSAGE: qtAddLibrary: found framework QtCore in directory /opt/local/Library/Frameworks :debug:configure Privilege de-escalation not attempted as not running as root. :debug:build build phase started at Wed Apr 9 14:06:46 CDT 2014 :notice:build ---> Building clustalx :debug:build Executing org.macports.build (clustalx) :debug:build Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9' :debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/clustalx-2.1" && /usr/bin/make -j8 -w all' :debug:build Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/clustalx-2.1" && /usr/bin/make -j8 -w all :info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/clustalx-2.1' :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o AlignmentParameters.o AlignmentParameters.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o AlignmentWidget.o AlignmentWidget.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o AlignOutputFileNames.o AlignOutputFileNames.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o ColorFileXmlParser.o ColorFileXmlParser.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o ColorParameters.o ColorParameters.cpp :info:build In file included from ColorParameters.cpp:1: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from ColorParameters.cpp:1: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from ColorParameters.cpp:1: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable] :info:build char temp = colorPar[i].consensusConditionList[j].toAscii(); :info:build ^ :info:build ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable] :info:build char showCon = consensus.toAscii(); :info:build ^ :info:build ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable] :info:build char showRes = res.toAscii(); :info:build ^ :info:build ColorParameters.cpp:160:18: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(i = 0; i < colorPar.size(); i++) :info:build ~ ^ ~~~~~~~~~~~~~~~ :info:build ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable] :info:build char temp = colorPar[i].consensusConditionList[j].toAscii(); :info:build ^ :info:build ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable] :info:build char showCon = consensus.toAscii(); :info:build ^ :info:build ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable] :info:build char showRes = res.toAscii(); :info:build ^ :info:build ColorParameters.cpp:197:18: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(i = 0; i < colorPar.size(); i++) :info:build ~ ^ ~~~~~~~~~~~~~~~ :info:build ColorParameters.cpp:229:22: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int i = 0; i < colors.size(); i++) :info:build ~ ^ ~~~~~~~~~~~~~ :info:build ColorParameters.cpp:238:22: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int i = 0; i < colors.size(); i++) :info:build ~ ^ ~~~~~~~~~~~~~ :info:build ColorParameters.cpp:251:37: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(colorNum > 0 && colorNum - 1 < colorPar.size()) :info:build ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~ :info:build In file included from ColorParameters.cpp:1: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 16 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o ColumnScoreParams.o ColumnScoreParams.cpp :info:build In file included from AlignmentViewerWidget.cpp:66: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignmentViewerWidget.cpp:66: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignmentWidget.cpp:49: :info:build In file included from ./AlignmentWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from AlignmentFormatOptions.cpp:11: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build : warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignmentWidget.cpp:49: :info:build In file included from ./AlignmentWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignOutputFileNames.cpp:26: :info:build In file included from ./AlignOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignmentFormatOptions.cpp:11: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warningIn file included from : unused variable 'y' [-Wunused-variable] :info:build AlignOutputFileNames.cpp: int y = x.size(); :info:build ^ :info:build 26: :info:build In file included from ./AlignOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from ColorFileXmlParser.cpp:3: :info:build In file included from ./ColorFileXmlParser.h:9: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignmentParameters.cpp:21: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from ColorFileXmlParser.cpp:3: :info:build In file included from ./ColorFileXmlParser.h:9: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignmentParameters.cpp:21: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from BootstrapTreeDialog.cpp:18: :info:build In file included from ./BootstrapTreeDialog.h:11: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from BootstrapTreeDialog.cpp:18: :info:build In file included from ./BootstrapTreeDialog.h:11: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from AlignmentViewerWidget.cpp:66: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from AlignOutputFileNames.cpp:26: :info:build In file included from ./AlignOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from AlignmentWidget.cpp:49: :info:build In file included from ./AlignmentWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from AlignmentParameters.cpp:22: :info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from ColorFileXmlParser.cpp:3: :info:build In file included from ./ColorFileXmlParser.h:9: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] :info:build void AlignmentParameters::showEvent(QShowEvent* event) :info:build ^ :info:build In file included from BootstrapTreeDialog.cpp:18: :info:build In file included from ./BootstrapTreeDialog.h:11: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build AlignmentWidget.cpp:67:7: warning: field 'blackAndWhite' will be initialized after field 'selectedColoredRes' [-Wreorder] :info:build blackAndWhite(false), :info:build ^ :info:build ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] :info:build QTreeWidgetItem *parentItem) :info:build ^ :info:build ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] :info:build void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) :info:build ^ :info:build ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] :info:build int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) :info:build ^ :info:build AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] :info:build int codeForSpace = clustalw::userParameters->resIndex( :info:build ^ :info:build AlignmentWidget.cpp:225:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] :info:build for(unsigned int j = 0; j < lengthLongestSeq; j++) :info:build ~ ^ ~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:235:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(code >= 0 && code < conservationPixmaps->size()) :info:build ~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:268:51: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) :info:build ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:280:51: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) :info:build ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:291:86: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] :info:build if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) :info:build ~~~~~~~~~~~~~~~~~~~~ ^ ~ :info:build AlignmentWidget.cpp:333:14: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(i < secStructPixmaps->size() && i < secStructInfo.size()) :info:build ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~ :info:build In file included from AlignmentFormatOptions.cpp:8: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from AlignmentFormatOptions.cpp:11: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build AlignmentWidget.cpp:569:36: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(selectedRes >= selectedColoredRes->size()) :info:build ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:689:30: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int j = 1; j <= strongGroup.size(); j++) :info:build ~ ^ ~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:693:30: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int j = 1; j <= weakGroup.size(); j++) :info:build ~ ^ ~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:700:35: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if((i + _fRes - 1 < (*alignment)[j].size()) && :info:build ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:701:35: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build (i + _fRes - 1 < (*alignment)[_fSeq].size())) :info:build ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:725:42: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int k = 1; k <= strongGroup.size(); k++) :info:build ~ ^ ~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:737:42: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int k = 1; k <= weakGroup.size(); k++) :info:build ~ ^ ~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:760:34: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int k = 1; k <= strongGroup.size(); k++) :info:build ~ ^ ~~~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:771:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int k = 1; k <= weakGroup.size(); k++) :info:build ~ ^ ~~~~~~~~~~~~~~~~ :info:build AlignmentWidget.cpp:878:24:AlignmentViewerWidget.cpp:588:37: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) :info:build ~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :info:build warningAlignmentWidget.cpp:927:28: : comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(i = 0; i < len && i < gapMask->size(); i++) :info:build ~ ^ ~~~~~~~~~~~~~~~ :info:build AlignmentViewerWidget.cpp:645:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for (i = 0; i < len && i < _secStructMask->size();i++) :info:build ~ ^ ~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentViewerWidget.cpp:652:37: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(i = 0; i < len && i < ssMask.size(); i++) :info:build ~ ^ ~~~~~~~~~~~~~ :info:build warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) :info:build ~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :info:build AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] :info:build void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) :info:build ^ :info:build AlignmentWidget.cpp:1039:26: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(int j = 0; j < aminoAcid.size(); j++) :info:build ~ ^ ~~~~~~~~~~~~~~~~ :info:build In file included from AlignmentParameters.cpp:14: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from AlignmentParameters.cpp:21: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from AlignOutputFileNames.cpp:23: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from AlignOutputFileNames.cpp:26: :info:build In file included from ./AlignOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from ColorFileXmlParser.cpp:1: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from ColorFileXmlParser.cpp:3: :info:build In file included from ./ColorFileXmlParser.h:9: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from BootstrapTreeDialog.cpp:15: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from BootstrapTreeDialog.cpp:18: :info:build In file included from ./BootstrapTreeDialog.h:11: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 4 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o FileDialog.o FileDialog.cpp :info:build In file included from AlignmentViewerWidget.cpp:63: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from AlignmentViewerWidget.cpp:66: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from AlignmentWidget.cpp:48: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from AlignmentWidget.cpp:49: :info:build In file included from ./AlignmentWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 7 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o HardCodedColorScheme.o HardCodedColorScheme.cpp :info:build 6 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o HelpDisplayWidget.o HelpDisplayWidget.cpp :info:build 9 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o HistogramWidget.o HistogramWidget.cpp :info:build 6 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o KeyController.o KeyController.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o LowScoringSegParams.o LowScoringSegParams.cpp :info:build 10 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o main.o main.cpp :info:build In file included from HardCodedColorScheme.cpp:1: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from HardCodedColorScheme.cpp:1: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from HardCodedColorScheme.cpp:1: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from HelpDisplayWidget.cpp:15: :info:build In file included from ./HelpDisplayWidget.h:17: :info:build In file included from ./clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from HelpDisplayWidget.cpp:15: :info:build In file included from ./HelpDisplayWidget.h:17: :info:build In file included from ./clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from HardCodedColorScheme.cpp:1: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from KeyController.cpp:9: :info:build In file included from ./KeyController.h:13: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QKeyEvent:1: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build 1 warning generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o mainwindow.o mainwindow.cpp :info:build In file included from ColumnScoreParams.cpp:22: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from HelpDisplayWidget.cpp:15: :info:build In file included from ./HelpDisplayWidget.h:18: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from ColumnScoreParams.cpp:22: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 5 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o PairwiseParams.o PairwiseParams.cpp :info:build 26 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o PostscriptFileParams.o PostscriptFileParams.cpp :info:build In file included from ColumnScoreParams.cpp:23: :info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] :info:build void ColumnScoreParams::showEvent(QShowEvent* event) :info:build ^ :info:build In file included from ColumnScoreParams.cpp:14: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from ColumnScoreParams.cpp:22: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 7 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o ProteinGapParameters.o ProteinGapParameters.cpp :info:build In file included from main.cpp:21: :info:build In file included from ./clustalW/substitutionMatrix/SubMatrix.h:28: :info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from main.cpp:21: :info:build In file included from ./clustalW/substitutionMatrix/SubMatrix.h:28: :info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from main.cpp:21: :info:build ./clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build ./clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from main.cpp:22: :info:build ./QTUtility.h:28:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual] :info:build virtual char promptForYesNo(char *title,char *prompt); :info:build ^ :info:build clustalW/general/Utility.h:43:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 2nd parameter ('const char *' vs 'char *') :info:build virtual char promptForYesNo(char *title, const char *prompt); :info:build ^ :info:build clustalW/general/Utility.h:44:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 1st parameter ('const char *' vs 'char *') :info:build virtual char promptForYesNo(const char *title, const char *prompt); :info:build ^ :info:build In file included from main.cpp:22: :info:build ./QTUtility.h:29:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual] :info:build virtual char promptForYesNo(const char *title,char *prompt); :info:build ^ :info:build clustalW/general/Utility.h:43:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 1st parameter ('char *' vs 'const char *') :info:build virtual char promptForYesNo(char *title, const char *prompt); :info:build ^ :info:build clustalW/general/Utility.h:44:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 2nd parameter ('const char *' vs 'char *') :info:build virtual char promptForYesNo(const char *title, const char *prompt); :info:build ^ :info:build In file included from PostscriptFileParams.cpp:1: :info:build In file included from ./PostscriptFileParams.h:4: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from PostscriptFileParams.cpp:1: :info:build In file included from ./PostscriptFileParams.h:4: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from PostscriptFileParams.cpp:1: :info:build In file included from ./PostscriptFileParams.h:4: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from PostscriptFileParams.cpp:1: :info:build In file included from ./PostscriptFileParams.h:4: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 5 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o PSPrinter.o PSPrinter.cpp :info:build HistogramWidget.cpp:180:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(column >= 0 && column < arrayOfHeights->size()) :info:build ~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~ :info:build HistogramWidget.cpp:198:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build if(column >= 0 && column < arrayOfHeights->size()) :info:build ~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~ :info:build In file included from HistogramWidget.cpp:24: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build 3 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o QTUtility.o QTUtility.cpp :info:build In file included from main.cpp:21: :info:build In file included from ./clustalW/substitutionMatrix/SubMatrix.h:28: :info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from main.cpp:24: :info:build In file included from ./mainwindow.h:37: :info:build In file included from ./AlignmentViewerWidget.h:37: :info:build In file included from ./AlignmentWidget.h:43: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QKeyEvent:1: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build 8 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Resources.o Resources.cpp :info:build In file included from HelpDisplayWidget.cpp:15: :info:build In file included from ./HelpDisplayWidget.h:17: :info:build In file included from ./clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from HelpDisplayWidget.cpp:19: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from LowScoringSegParams.cpp:22: :info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8: :info:build In file included from clustalW/substitutionMatrix/SubMatrix.h:28: :info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from LowScoringSegParams.cpp:22: :info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8: :info:build In file included from clustalW/substitutionMatrix/SubMatrix.h:28: :info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 6 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o SaveSeqFile.o SaveSeqFile.cpp :info:build In file included from LowScoringSegParams.cpp:22: :info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] :info:build void LowScoringSegParams::showEvent(QShowEvent* event) :info:build ^ :info:build In file included from LowScoringSegParams.cpp:15: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from LowScoringSegParams.cpp:22: :info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8: :info:build In file included from clustalW/substitutionMatrix/SubMatrix.h:28: :info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 7 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o SearchForString.o SearchForString.cpp :info:build In file included from mainwindow.cpp:98: :info:build In file included from ./mainwindow.h:37: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from mainwindow.cpp:98: :info:build In file included from ./mainwindow.h:37: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from QTUtility.cpp:7: :info:build In file included from ./QTUtility.h:11: :info:build In file included from ./clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from QTUtility.cpp:7: :info:build In file included from ./QTUtility.h:11: :info:build In file included from ./clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from PairwiseParams.cpp:22: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from PairwiseParams.cpp:22: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from mainwindow.cpp:98: :info:build In file included from ./mainwindow.h:37: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from QTUtility.cpp:7: :info:build ./QTUtility.h:28:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual] :info:build virtual char promptForYesNo(char *title,char *prompt); :info:build ^ :info:build ./clustalW/general/Utility.h:43:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 2nd parameter ('const char *' vs 'char *') :info:build virtual char promptForYesNo(char *title, const char *prompt); :info:build ^ :info:build ./clustalW/general/Utility.h:44:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 1st parameter ('const char *' vs 'char *') :info:build virtual char promptForYesNo(const char *title, const char *prompt); :info:build ^ :info:build In file included from QTUtility.cpp:7: :info:build ./QTUtility.h:29:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual] :info:build virtual char promptForYesNo(const char *title,char *prompt); :info:build ^ :info:build ./clustalW/general/Utility.h:43:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 1st parameter ('char *' vs 'const char *') :info:build virtual char promptForYesNo(char *title, const char *prompt); :info:build ^ :info:build ./clustalW/general/Utility.h:44:22: note: hidden overloaded virtual function 'clustalw::Utility::promptForYesNo' declared here: type mismatch at 2nd parameter ('const char *' vs 'char *') :info:build virtual char promptForYesNo(const char *title, const char *prompt); :info:build ^ :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o SecStructOptions.o SecStructOptions.cpp :info:build In file included from PairwiseParams.cpp:23: :info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from QTUtility.cpp:7: :info:build In file included from ./QTUtility.h:11: :info:build In file included from ./clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] :info:build void PairwiseParams::showEvent(QShowEvent* event) :info:build ^ :info:build mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter] :info:build void MainWindow::showEvent(QShowEvent* event) :info:build ^ :info:build In file included from PairwiseParams.cpp:21: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from PairwiseParams.cpp:22: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 5 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o SeqNameWidget.o SeqNameWidget.cpp :info:build mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] :info:build void MainWindow::writeViewer1AsPostscript(int type) :info:build ^ :info:build In file included from ProteinGapParameters.cpp:13: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from ProteinGapParameters.cpp:13: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 7 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o TreeFormatOptions.o TreeFormatOptions.cpp :info:build In file included from mainwindow.cpp:90: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from mainwindow.cpp:98: :info:build In file included from ./mainwindow.h:37: :info:build In file included from ./AlignmentViewerWidget.h:36: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from ProteinGapParameters.cpp:8: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from ProteinGapParameters.cpp:13: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 4 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o TreeOutputFileNames.o TreeOutputFileNames.cpp :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o WritePostscriptFile.o WritePostscriptFile.cpp :info:build In file included from PSPrinter.cpp:20: :info:build In file included from ./PSPrinter.h:11: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from PSPrinter.cpp:20: :info:build In file included from ./PSPrinter.h:11: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from PSPrinter.cpp:20: :info:build In file included from ./PSPrinter.h:11: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] :info:build int err; :info:build ^ :info:build PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] :info:build int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local :info:build ^ :info:build PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] :info:build int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local :info:build ^ :info:build PSPrinter.cpp:207:55: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare] :info:build if(res.isLetter() && resNumber.size() > i - data->firstSeq) :info:build ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~ :info:build PSPrinter.cpp:307:67: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare] :info:build if(res.isLetter() && resNumber.size() > seq) :info:build ~~~~~~~~~~~~~~~~ ^ ~~~ :info:build PSPrinter.cpp:421:67: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare] :info:build if(res.isLetter() && resNumber.size() > i) :info:build ~~~~~~~~~~~~~~~~ ^ ~ :info:build PSPrinter.cpp:587:32: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare] :info:build if(data->nameHeader.size() > ix) :info:build ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ :info:build PSPrinter.cpp:730:30: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(i = fr; i <= lr && i < ruler.length(); i++) :info:build ~ ^ ~~~~~~~~~~~~~~ :info:build PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] :info:build int psX, psY, curveBottom; :info:build ^ :info:build PSPrinter.cpp:789:34: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare] :info:build for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) :info:build ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~ :info:build In file included from PSPrinter.cpp:19: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from PSPrinter.cpp:20: :info:build In file included from ./PSPrinter.h:11: :info:build In file included from ./ColorParameters.h:11: :info:build In file included from ./HardCodedColorScheme.h:8: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from SaveSeqFile.cpp:23: :info:build In file included from ./SaveSeqFile.h:9: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from SaveSeqFile.cpp:23: :info:build In file included from ./SaveSeqFile.h:9: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from SaveSeqFile.cpp:23: :info:build In file included from ./SaveSeqFile.h:9: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from SaveSeqFile.cpp:21: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from SaveSeqFile.cpp:23: :info:build In file included from ./SaveSeqFile.h:9: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 16 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Clustal.o clustalW/Clustal.cpp :info:build 6 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Help.o clustalW/Help.cpp :info:build In file included from SecStructOptions.cpp:12: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from SecStructOptions.cpp:12: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from SeqNameWidget.cpp:59: :info:build In file included from ./SeqNameWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from SeqNameWidget.cpp:59: :info:build In file included from ./SeqNameWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from SecStructOptions.cpp:8: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from SecStructOptions.cpp:12: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from SeqNameWidget.cpp:59: :info:build In file included from ./SeqNameWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build SeqNameWidget.cpp:375:11: warning: unused variable 'redrawRect' [-Wunused-variable] :info:build QRect redrawRect = event->rect(); :info:build ^ :info:build 4 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Alignment.o clustalW/alignment/Alignment.cpp :info:build In file included from TreeFormatOptions.cpp:11: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from TreeFormatOptions.cpp:11: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 8 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp :info:build In file included from SeqNameWidget.cpp:58: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from SeqNameWidget.cpp:59: :info:build In file included from ./SeqNameWidget.h:41: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/Clustal.cpp:27: :info:build In file included from clustalW/Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from TreeFormatOptions.cpp:7: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from TreeFormatOptions.cpp:11: :info:build In file included from ./clustalW/general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/Clustal.cpp:27: :info:build In file included from clustalW/Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 7 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp :info:build 4 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Sequence.o clustalW/alignment/Sequence.cpp :info:build In file included from clustalW/Clustal.cpp:27: :info:build In file included from clustalW/Clustal.h:18: :info:build In file included from clustalW/fileInput/FileReader.h:12: :info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from TreeOutputFileNames.cpp:17: :info:build In file included from ./TreeOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from TreeOutputFileNames.cpp:17: :info:build In file included from ./TreeOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from WritePostscriptFile.cpp:24: :info:build In file included from ./WritePostscriptFile.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from WritePostscriptFile.cpp:24: :info:build In file included from ./WritePostscriptFile.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from TreeOutputFileNames.cpp:17: :info:build In file included from ./TreeOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from clustalW/Clustal.cpp:27: :info:build In file included from clustalW/Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp :info:build In file included from WritePostscriptFile.cpp:24: :info:build In file included from ./WritePostscriptFile.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from TreeOutputFileNames.cpp:14: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from TreeOutputFileNames.cpp:17: :info:build In file included from ./TreeOutputFileNames.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/alignment/Alignment.cpp:25: :info:build In file included from clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/alignment/Alignment.cpp:25: :info:build In file included from clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27: :info:build In file included from clustalW/alignment/AlignmentOutput.h:24: :info:build In file included from clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27: :info:build In file included from clustalW/alignment/Alignment.cpp:25: :info:build In file included from clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out");In file included from clustalW/alignment/AlignmentOutput.h:24: :info:build In file included from clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from WritePostscriptFile.cpp:21: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62: :info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52: :info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field] :info:build char type; :info:build ^ :info:build In file included from WritePostscriptFile.cpp:24: :info:build In file included from ./WritePostscriptFile.h:10: :info:build In file included from ./ClustalQtParams.h:13: :info:build In file included from ./clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27: :info:build In file included from clustalW/alignment/AlignmentOutput.h:24: :info:build In file included from clustalW/alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable] :info:build SeqArray::iterator posToAddTo = sectionToRealign.begin(); :info:build ^ :info:build 6 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp :info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10: :info:build In file included from clustalW/alignment/ObjectiveScore.h:14: :info:build In file included from clustalW/alignment/../general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/alignment/Sequence.cpp:10: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10: :info:build In file included from clustalW/alignment/ObjectiveScore.h:14: :info:build In file included from clustalW/alignment/../general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/alignment/Sequence.cpp:10: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/alignment/Alignment.cpp:25: :info:build In file included from clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10: :info:build In file included from clustalW/alignment/ObjectiveScore.h:15: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from clustalW/alignment/Sequence.cpp:10: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10: :info:build In file included from clustalW/alignment/ObjectiveScore.h:14: :info:build In file included from clustalW/alignment/../general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10: :info:build clustalW/alignment/ObjectiveScore.h:40:14: warning: private field 'scale' is not used [-Wunused-private-field] :info:build long scale; :info:build ^ :info:build clustalW/alignment/ObjectiveScore.h:41:13: warning: private field 'weightScale' is not used [-Wunused-private-field] :info:build int weightScale; :info:build ^ :info:build clustalW/alignment/ObjectiveScore.h:42:13: warning: private field 'sagaGapEx' is not used [-Wunused-private-field] :info:build int sagaGapEx, sagaGapOp; :info:build ^ :info:build clustalW/alignment/ObjectiveScore.h:42:24: warning: private field 'sagaGapOp' is not used [-Wunused-private-field] :info:build int sagaGapEx, sagaGapOp; :info:build ^ :info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27: :info:build In file included from clustalW/alignment/AlignmentOutput.h:24: :info:build In file included from clustalW/alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 6 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o FileParser.o clustalW/fileInput/FileParser.cpp :info:build In file included from clustalW/fileInput/ClustalFileParser.cpp:19: :info:build In file included from clustalW/fileInput/ClustalFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 9 warnings generated. :info:build In file included from clustalW/fileInput/ClustalFileParser.cpp:19: :info:build In file included from clustalW/fileInput/ClustalFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o FileReader.o clustalW/fileInput/FileReader.cpp :info:build 3 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp :info:build In file included from clustalW/fileInput/ClustalFileParser.cpp:19: :info:build In file included from clustalW/fileInput/ClustalFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/fileInput/EMBLFileParser.cpp:16: :info:build In file included from clustalW/fileInput/EMBLFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/EMBLFileParser.cpp:16: :info:build In file included from clustalW/fileInput/EMBLFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 3 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o InFileStream.o clustalW/fileInput/InFileStream.cpp :info:build In file included from clustalW/fileInput/EMBLFileParser.cpp:16: :info:build In file included from clustalW/fileInput/EMBLFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 5 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp :info:build In file included from clustalW/fileInput/FileParser.cpp:14: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/FileParser.cpp:14: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/FileReader.cpp:29: :info:build In file included from clustalW/fileInput/FileReader.h:12: :info:build In file included from clustalW/fileInput/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/FileReader.cpp:29: :info:build In file included from clustalW/fileInput/FileReader.h:12: :info:build In file included from clustalW/fileInput/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/GDEFileParser.cpp:16: :info:build In file included from clustalW/fileInput/GDEFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/GDEFileParser.cpp:16: :info:build In file included from clustalW/fileInput/GDEFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/FileParser.cpp:14: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/fileInput/FileReader.cpp:29: :info:build In file included from clustalW/fileInput/FileReader.h:12: :info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build 3 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp :info:build In file included from clustalW/fileInput/GDEFileParser.cpp:16: :info:build In file included from clustalW/fileInput/GDEFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 3 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp :info:build In file included from clustalW/fileInput/FileReader.cpp:29: :info:build In file included from clustalW/fileInput/FileReader.h:12: :info:build In file included from clustalW/fileInput/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 3 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp :info:build In file included from clustalW/fileInput/MSFFileParser.cpp:16: :info:build In file included from clustalW/fileInput/MSFFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/MSFFileParser.cpp:16: :info:build In file included from clustalW/fileInput/MSFFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o ClustalWResources.o clustalW/general/ClustalWResources.cpp :info:build clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] :info:build vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) :info:build ^ :info:build clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] :info:build void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, :info:build ^ :info:build clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] :info:build void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, :info:build ^ :info:build clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter] :info:build string& secStructName, int &structPenalties, int length) :info:build ^ :info:build clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] :info:build string& secStructName, int &structPenalties, int length) :info:build ^ :info:build 5 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o DebugLog.o clustalW/general/DebugLog.cpp :info:build In file included from clustalW/fileInput/MSFFileParser.cpp:16: :info:build In file included from clustalW/fileInput/MSFFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/fileInput/PearsonFileParser.cpp:26: :info:build In file included from clustalW/fileInput/PearsonFileParser.h:14: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/PearsonFileParser.cpp:26: :info:build In file included from clustalW/fileInput/PearsonFileParser.h:14: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 5 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o OutputFile.o clustalW/general/OutputFile.cpp :info:build 6 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Stats.o clustalW/general/Stats.cpp :info:build In file included from clustalW/fileInput/PIRFileParser.cpp:16: :info:build In file included from clustalW/fileInput/PIRFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/PIRFileParser.cpp:16: :info:build In file included from clustalW/fileInput/PIRFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter] :info:build Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) :info:build ^ :info:build clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] :info:build void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, :info:build ^ :info:build clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter] :info:build vector& secStructMask, string& secStructName, :info:build ^ :info:build clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter] :info:build vector& secStructMask, string& secStructName, :info:build ^ :info:build clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] :info:build int &structPenalties, int length) :info:build ^ :info:build In file included from clustalW/fileInput/PearsonFileParser.cpp:26: :info:build In file included from clustalW/fileInput/PearsonFileParser.h:14: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 8 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o SymMatrix.o clustalW/general/SymMatrix.cpp :info:build clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] :info:build void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, :info:build ^ :info:build clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] :info:build void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, :info:build ^ :info:build clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter 'secStructName' [-Wunused-parameter] :info:build string& secStructName, int &structPenalties, int length) :info:build ^ :info:build clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter] :info:build string& secStructName, int &structPenalties, int length) :info:build ^ :info:build In file included from clustalW/fileInput/PIRFileParser.cpp:16: :info:build In file included from clustalW/fileInput/PIRFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/fileInput/RSFFileParser.cpp:16: :info:build In file included from clustalW/fileInput/RSFFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/fileInput/RSFFileParser.cpp:16: :info:build In file included from clustalW/fileInput/RSFFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/general/ClustalWResources.cpp:14: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 7 warnings generated. :info:build In file included from clustalW/general/ClustalWResources.cpp:14: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] :info:build void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, :info:build ^ :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o UserParameters.o clustalW/general/UserParameters.cpp :info:build In file included from clustalW/fileInput/RSFFileParser.cpp:16: :info:build In file included from clustalW/fileInput/RSFFileParser.h:10: :info:build In file included from clustalW/fileInput/FileParser.h:22: :info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build clustalW/general/ClustalWResources.cpp:106:5: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds] :info:build delim[1] = 0; :info:build ^ ~ :info:build clustalW/general/ClustalWResources.cpp:104:5: note: array 'delim' declared here :info:build char delim[1]; :info:build ^ :info:build In file included from clustalW/general/ClustalWResources.cpp:14: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 8 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Utility.o clustalW/general/Utility.cpp :info:build In file included from clustalW/general/OutputFile.cpp:10: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/general/OutputFile.cpp:10: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/general/Stats.cpp:15: :info:build In file included from clustalW/general/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/general/Stats.cpp:15: :info:build In file included from clustalW/general/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/general/OutputFile.cpp:10: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/general/Stats.cpp:15: :info:build In file included from clustalW/general/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build 4 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp :info:build In file included from clustalW/general/Stats.cpp:15: :info:build In file included from clustalW/general/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp :info:build 4 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp :info:build In file included from clustalW/general/SymMatrix.cpp:10: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 1 warning generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o Iteration.o clustalW/multipleAlign/Iteration.cpp :info:build In file included from clustalW/general/VectorOutOfRange.cpp:9: :info:build clustalW/general/VectorOutOfRange.h:23:21: error: implicit instantiation of undefined template 'std::__1::basic_string, std::__1::allocator >' :info:build std::string _name; :info:build ^ :info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:188:33: note: template is declared here :info:build class _LIBCPP_TYPE_VIS_ONLY basic_string; :info:build ^ :info:build In file included from clustalW/general/VectorOutOfRange.cpp:9: :info:build clustalW/general/VectorOutOfRange.h:14:38: error: implicit instantiation of undefined template 'std::__1::basic_string, std::__1::allocator >' :info:build VectorOutOfRange(std::string vectorName, int index, int max) :info:build ^ :info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:188:33: note: template is declared here :info:build class _LIBCPP_TYPE_VIS_ONLY basic_string; :info:build ^ :info:build In file included from clustalW/general/VectorOutOfRange.cpp:9: :info:build clustalW/general/VectorOutOfRange.h:14:38: warning: unused parameter 'vectorName' [-Wunused-parameter] :info:build VectorOutOfRange(std::string vectorName, int index, int max) :info:build ^ :info:build 3 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp :info:build 5 warnings generated. :info:build /usr/bin/clang++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.9 -Wall -W -DOS_UNIX -DOS_MAC -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/opt/local/share/qt4/mkspecs/macx-g++ -I. -I. -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/opt/local/Library/Frameworks/QtXml.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers -I/opt/local/Library/Frameworks/QtCore.framework/Versions/4/Headers -I/opt/local/include -o MSA.o clustalW/multipleAlign/MSA.cpp :info:build In file included from clustalW/general/UserParameters.cpp:24: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/general/UserParameters.cpp:24: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] :info:build UserParameters::UserParameters(bool log) :info:build ^ :info:build In file included from clustalW/general/UserParameters.cpp:24: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/general/Utility.cpp:19: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/general/Utility.cpp:19: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] :info:build void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) :info:build ^ :info:build In file included from clustalW/general/Utility.cpp:19: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 1 warning and 2 errors generated. :info:build make: *** [VectorOutOfRange.o] Error 1 :info:build make: *** Waiting for unfinished jobs.... :info:build In file included from clustalW/interface/InteractiveMenu.cpp:23: :info:build In file included from clustalW/interface/InteractiveMenu.h:15: :info:build In file included from clustalW/interface/../Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/interface/InteractiveMenu.cpp:23: :info:build In file included from clustalW/interface/InteractiveMenu.h:15: :info:build In file included from clustalW/interface/../Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/interface/CommandLineParser.cpp:13: :info:build In file included from clustalW/interface/CommandLineParser.h:18: :info:build In file included from clustalW/interface/../Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/multipleAlign/Iteration.cpp:13: :info:build In file included from clustalW/multipleAlign/Iteration.h:8: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/multipleAlign/Iteration.cpp:13: :info:build In file included from clustalW/multipleAlign/Iteration.h:8: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/interface/CommandLineParser.cpp:13: :info:build In file included from clustalW/interface/CommandLineParser.h:18: :info:build In file included from clustalW/interface/../Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/interface/InteractiveMenu.cpp:23: :info:build In file included from clustalW/interface/InteractiveMenu.h:15: :info:build In file included from clustalW/interface/../Clustal.h:18: :info:build In file included from clustalW/fileInput/FileReader.h:12: :info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from clustalW/multipleAlign/Iteration.cpp:13: :info:build In file included from clustalW/multipleAlign/Iteration.h:84 warnings generated. :info:build : :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from clustalW/interface/CommandLineParser.cpp:13: :info:build In file included from clustalW/interface/CommandLineParser.h:18: :info:build In file included from clustalW/interface/../Clustal.h:18: :info:build In file included from clustalW/fileInput/FileReader.h:12: :info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build clustalW/multipleAlign/Iteration.cpp:231:17: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] :info:build tmpnam (buffer); :info:build ^ :info:build /usr/include/stdio.h:274:7: note: 'tmpnam' declared here :info:build char *tmpnam(char *); :info:build ^ :info:build In file included from clustalW/multipleAlign/MSA.cpp:16: :info:build In file included from clustalW/multipleAlign/MSA.h:10: :info:build In file included from clustalW/multipleAlign/ProfileBase.h:14: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:42: :info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build In file included from clustalW/multipleAlign/MSA.cpp:16: :info:build In file included from clustalW/multipleAlign/MSA.h:10: :info:build In file included from clustalW/multipleAlign/ProfileBase.h:14: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:43: :info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] :info:build int y = x.size(); :info:build ^ :info:build 4 warnings generated. :info:build In file included from clustalW/multipleAlign/Iteration.cpp:13: :info:build In file included from clustalW/multipleAlign/Iteration.h:8: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from clustalW/multipleAlign/MSA.cpp:16: :info:build In file included from clustalW/multipleAlign/MSA.h:10: :info:build In file included from clustalW/multipleAlign/ProfileBase.h:14: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:42: :info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8: :info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printInFormat(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] :info:build void printVectorToFile(vector& temp, char* name = "tempfile.out"); :info:build ^ :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: :info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] :info:build int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 :info:build ^ :info:build clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] :info:build string phylipName) :info:build ^ :info:build In file included from clustalW/interface/CommandLineParser.cpp:13: :info:build In file included from clustalW/interface/CommandLineParser.h:18: :info:build In file included from clustalW/interface/../Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/multipleAlign/MSA.cpp:16: :info:build In file included from clustalW/multipleAlign/MSA.h:10: :info:build In file included from clustalW/multipleAlign/ProfileBase.h:14: :info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41: :info:build In file included from clustalW/alignment/Sequence.h:20: :info:build In file included from clustalW/alignment/../general/userparams.h:8: :info:build In file included from clustalW/general/UserParameters.h:22: :info:build In file included from clustalW/general/utils.h:8: :info:build In file included from clustalW/general/Utility.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build In file included from clustalW/interface/InteractiveMenu.cpp:23: :info:build In file included from clustalW/interface/InteractiveMenu.h:15: :info:build In file included from clustalW/interface/../Clustal.h:15: :info:build In file included from clustalW/general/clustalw.h:44: :info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] :info:build int firstSeq, numSeqsInSub; :info:build ^ :info:build 5 warnings generated. :info:build 7 warnings generated. :info:build 5 warnings generated. :info:build 6 warnings generated. :info:build 5 warnings generated. :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/clustalx-2.1' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/work/clustalx-2.1" && /usr/bin/make -j8 -w all :info:build Exit code: 2 :error:build org.macports.build for port clustalx returned: command execution failed :debug:build Error code: CHILDSTATUS 18287 2 :debug:build Backtrace: command execution failed while executing "system -nice 0 $fullcmdstring" ("eval" body line 1) invoked from within "eval system $notty $nice \$fullcmdstring" invoked from within "command_exec build" (procedure "portbuild::build_main" line 8) invoked from within "$procedure $targetname" :info:build Warning: targets not executed for clustalx: org.macports.activate org.macports.build org.macports.destroot org.macports.install :notice:build Please see the log file for port clustalx for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/main.log