Ticket #43306: main.log

File main.log, 236.7 KB (added by pst@…, 12 years ago)

Build error log for clustalx

Line 
1version:1
2:msg:main --->  Computing dependencies for clustalx:info:main .:debug:main clustalx has no conflicts
3:debug:main Searching for dependency: qt4-mac
4:debug:main Didn't find receipt, going to depspec regex for: qt4-mac
5:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/aqua/qt4-mac
6:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
7:debug:main compiler clang 503.0.38 not blacklisted because it doesn't match { clang <= 318.0.61 }
8:debug:main adding the default universal variant
9:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
10:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
11:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
12:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
13:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
14:info:main .:debug:main Checking for conflicts against qt4-mac
15:debug:main Searching for dependency: qt3
16:debug:main Didn't find receipt, going to depspec regex for: qt3
17:debug:main Searching for dependency: qt3-mac
18:debug:main Didn't find receipt, going to depspec regex for: qt3-mac
19:debug:main Searching for dependency: zlib
20:debug:main Found Dependency: receipt exists for zlib
21:debug:main Searching for dependency: dbus
22:debug:main Didn't find receipt, going to depspec regex for: dbus
23:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/dbus
24:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
25:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
26:debug:main universal variant already exists, so not adding the default one
27:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
28:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
29:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
30:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
31:debug:main Searching for dependency: openssl
32:debug:main Found Dependency: receipt exists for openssl
33:debug:main Searching for dependency: tiff
34:debug:main Didn't find receipt, going to depspec regex for: tiff
35:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/tiff
36:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
37:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
38:debug:main universal variant already exists, so not adding the default one
39:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
40:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
41:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
42:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
43:debug:main Searching for dependency: libpng
44:debug:main Didn't find receipt, going to depspec regex for: libpng
45:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/libpng
46:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
47:debug:main adding the default universal variant
48:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
49:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
50:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
51:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
52:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
53:debug:main Searching for dependency: libmng
54:debug:main Didn't find receipt, going to depspec regex for: libmng
55:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/libmng
56:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
57:debug:main adding the default universal variant
58:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
59:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
60:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
61:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
62:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
63:debug:main Searching for dependency: jpeg
64:debug:main Didn't find receipt, going to depspec regex for: jpeg
65:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/jpeg
66:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
67:debug:main adding the default universal variant
68:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
69:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
70:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
71:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
72:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
73:info:main .:debug:main Checking for conflicts against dbus
74:debug:main Searching for dependency: dbus-devel
75:debug:main Didn't find receipt, going to depspec regex for: dbus-devel
76:debug:main Searching for dependency: expat
77:debug:main Found Dependency: receipt exists for expat
78:info:main .:debug:main tiff has no conflicts
79:debug:main Searching for dependency: xz
80:debug:main Didn't find receipt, going to depspec regex for: xz
81:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/xz
82:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
83:debug:main adding the default universal variant
84:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
85:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
86:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
87:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
88:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
89:info:main .:debug:main xz has no conflicts
90:debug:main Searching for dependency: libiconv
91:debug:main Found Dependency: receipt exists for libiconv
92:debug:main Searching for dependency: gettext
93:debug:main Found Dependency: receipt exists for gettext
94:info:main .:debug:main libpng has no conflicts
95:info:main .:debug:main libmng has no conflicts
96:debug:main Searching for dependency: lcms
97:debug:main Didn't find receipt, going to depspec regex for: lcms
98:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/lcms
99:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
100:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
101:debug:main universal variant already exists, so not adding the default one
102:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
103:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
104:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
105:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
106:info:main .:debug:main lcms has no conflicts
107:info:main .:debug:main Checking for conflicts against jpeg
108:debug:main Searching for dependency: libjpeg-turbo
109:debug:main Didn't find receipt, going to depspec regex for: libjpeg-turbo
110:debug:main Searching for dependency: mozjpeg
111:debug:main Didn't find receipt, going to depspec regex for: mozjpeg
112:msg:main
113:msg:main --->  Dependencies to be installed: qt4-mac dbus jpeg libmng lcms tiff xz libpng
114:debug:main Starting logging for dbus
115:debug:clean Starting logging for jpeg
116:debug:clean Starting logging for xz
117:debug:clean Starting logging for tiff
118:debug:clean Starting logging for lcms
119:debug:clean Starting logging for libmng
120:debug:clean Starting logging for libpng
121:debug:clean Starting logging for qt4-mac
122:debug:main Executing org.macports.main (clustalx)
123:debug:main changing euid/egid - current euid: 0 - current egid: 0
124:debug:main egid changed to: 501
125:debug:main euid changed to: 502
126:debug:archivefetch archivefetch phase started at Wed Apr  9 14:06:41 CDT 2014
127:msg:archivefetch --->  Fetching archive for clustalx
128:debug:archivefetch Executing org.macports.archivefetch (clustalx)
129:debug:archivefetch euid/egid changed to: 0/0
130:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
131:debug:archivefetch euid/egid changed to: 502/501
132:info:archivefetch --->  clustalx-2.1_0.darwin_13.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
133:msg:archivefetch --->  Attempting to fetch clustalx-2.1_0.darwin_13.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/clustalx
134:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
135:msg:archivefetch --->  Attempting to fetch clustalx-2.1_0.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/clustalx
136:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
137: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
138:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
139:debug:archivefetch Privilege de-escalation not attempted as not running as root.
140:debug:fetch fetch phase started at Wed Apr  9 14:06:42 CDT 2014
141:notice:fetch --->  Fetching distfiles for clustalx
142:debug:fetch Can't run fetch on this port without elevated privileges. Escalating privileges back to root.
143:debug:fetch euid changed to: 0. egid changed to: 0.
144:debug:fetch changing euid/egid - current euid: 0 - current egid: 0
145:debug:fetch egid changed to: 501
146:debug:fetch euid changed to: 502
147:debug:fetch Executing org.macports.fetch (clustalx)
148:info:fetch --->  clustalx-2.1.tar.gz doesn't seem to exist in /opt/local/var/macports/distfiles/clustalx
149:notice:fetch --->  Attempting to fetch clustalx-2.1.tar.gz from http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/clustalx
150:debug:fetch Privilege de-escalation not attempted as not running as root.
151:debug:checksum checksum phase started at Wed Apr  9 14:06:45 CDT 2014
152:notice:checksum --->  Verifying checksums for clustalx
153:debug:checksum Executing org.macports.checksum (clustalx)
154:info:checksum --->  Checksumming clustalx-2.1.tar.gz
155:debug:checksum Correct (rmd160) checksum for clustalx-2.1.tar.gz
156:debug:checksum Correct (sha256) checksum for clustalx-2.1.tar.gz
157:debug:checksum Privilege de-escalation not attempted as not running as root.
158:debug:extract extract phase started at Wed Apr  9 14:06:45 CDT 2014
159:notice:extract --->  Extracting clustalx
160:debug:extract Executing org.macports.extract (clustalx)
161:info:extract --->  Extracting clustalx-2.1.tar.gz
162:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/clustalx/clustalx-2.1.tar.gz'
163: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'
164: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 -'
165: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 -
166:debug:extract euid/egid changed to: 0/0
167: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
168:debug:extract euid/egid changed to: 502/501
169:debug:extract Privilege de-escalation not attempted as not running as root.
170:debug:patch patch phase started at Wed Apr  9 14:06:45 CDT 2014
171:debug:patch Executing org.macports.patch (clustalx)
172:debug:patch Privilege de-escalation not attempted as not running as root.
173:debug:configure configure phase started at Wed Apr  9 14:06:45 CDT 2014
174:notice:configure --->  Configuring clustalx
175:debug:configure Using compiler 'Xcode Clang'
176:debug:configure Executing org.macports.configure (clustalx)
177: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'
178: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'
179: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
180:info:configure Project MESSAGE: qtAddLibrary: found framework QtXml in directory /opt/local/Library/Frameworks
181:info:configure Project MESSAGE: qtAddLibrary: found framework QtGui in directory /opt/local/Library/Frameworks
182:info:configure Project MESSAGE: qtAddLibrary: found framework QtCore in directory /opt/local/Library/Frameworks
183:debug:configure Privilege de-escalation not attempted as not running as root.
184:debug:build build phase started at Wed Apr  9 14:06:46 CDT 2014
185:notice:build --->  Building clustalx
186:debug:build Executing org.macports.build (clustalx)
187: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'
188: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'
189: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
190: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'
191: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
192: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
193: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
194: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
195: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
196: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
197: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
198: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
199:info:build In file included from ColorParameters.cpp:1:
200:info:build In file included from ./ColorParameters.h:11:
201:info:build In file included from ./HardCodedColorScheme.h:8:
202:info:build In file included from ./ClustalQtParams.h:13:
203:info:build In file included from ./clustalW/alignment/Alignment.h:41:
204:info:build In file included from clustalW/alignment/Sequence.h:20:
205:info:build In file included from clustalW/alignment/../general/userparams.h:8:
206:info:build In file included from clustalW/general/UserParameters.h:22:
207:info:build In file included from clustalW/general/utils.h:8:
208:info:build In file included from clustalW/general/Utility.h:15:
209:info:build In file included from clustalW/general/clustalw.h:42:
210:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
211:info:build            int y = x.size();
212:info:build                ^
213:info:build In file included from ColorParameters.cpp:1:
214:info:build In file included from ./ColorParameters.h:11:
215:info:build In file included from ./HardCodedColorScheme.h:8:
216:info:build In file included from ./ClustalQtParams.h:13:
217:info:build In file included from ./clustalW/alignment/Alignment.h:41:
218:info:build In file included from clustalW/alignment/Sequence.h:20:
219:info:build In file included from clustalW/alignment/../general/userparams.h:8:
220:info:build In file included from clustalW/general/UserParameters.h:22:
221:info:build In file included from clustalW/general/utils.h:8:
222:info:build In file included from clustalW/general/Utility.h:15:
223:info:build In file included from clustalW/general/clustalw.h:43:
224:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
225:info:build            int y = x.size();
226:info:build                ^
227:info:build In file included from ColorParameters.cpp:1:
228:info:build In file included from ./ColorParameters.h:11:
229:info:build In file included from ./HardCodedColorScheme.h:8:
230:info:build In file included from ./ClustalQtParams.h:13:
231:info:build In file included from ./clustalW/alignment/Alignment.h:42:
232:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
233:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
234:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
235:info:build                                                              ^
236:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
237:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
238:info:build                                                                  ^
239:info:build ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable]
240:info:build                     char temp = colorPar[i].consensusConditionList[j].toAscii();
241:info:build                          ^
242:info:build ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable]
243:info:build     char showCon = consensus.toAscii();
244:info:build          ^
245:info:build ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable]
246:info:build     char showRes = res.toAscii();
247:info:build          ^
248:info:build ColorParameters.cpp:160:18: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
249:info:build     for(i = 0; i < colorPar.size(); i++)
250:info:build                ~ ^ ~~~~~~~~~~~~~~~
251:info:build ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable]
252:info:build                     char temp = colorPar[i].consensusConditionList[j].toAscii();
253:info:build                          ^
254:info:build ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable]
255:info:build     char showCon = consensus.toAscii();
256:info:build          ^
257:info:build ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable]
258:info:build     char showRes = res.toAscii();
259:info:build          ^
260:info:build ColorParameters.cpp:197:18: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
261:info:build     for(i = 0; i < colorPar.size(); i++)
262:info:build                ~ ^ ~~~~~~~~~~~~~~~
263:info:build ColorParameters.cpp:229:22: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
264:info:build     for(int i = 0; i < colors.size(); i++)
265:info:build                    ~ ^ ~~~~~~~~~~~~~
266:info:build ColorParameters.cpp:238:22: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
267:info:build     for(int i = 0; i < colors.size(); i++)
268:info:build                    ~ ^ ~~~~~~~~~~~~~
269:info:build ColorParameters.cpp:251:37: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
270:info:build     if(colorNum > 0 && colorNum - 1 < colorPar.size())
271:info:build                        ~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~
272:info:build In file included from ColorParameters.cpp:1:
273:info:build In file included from ./ColorParameters.h:11:
274:info:build In file included from ./HardCodedColorScheme.h:8:
275:info:build In file included from ./ClustalQtParams.h:13:
276:info:build In file included from ./clustalW/alignment/Alignment.h:41:
277:info:build In file included from clustalW/alignment/Sequence.h:20:
278:info:build In file included from clustalW/alignment/../general/userparams.h:8:
279:info:build In file included from clustalW/general/UserParameters.h:22:
280:info:build In file included from clustalW/general/utils.h:8:
281:info:build In file included from clustalW/general/Utility.h:15:
282:info:build In file included from clustalW/general/clustalw.h:44:
283:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
284:info:build         int firstSeq, numSeqsInSub;
285:info:build             ^
286:info:build 16 warnings generated.
287: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
288:info:build In file included from AlignmentViewerWidget.cpp:66:
289:info:build In file included from ./AlignmentViewerWidget.h:36:
290:info:build In file included from ./clustalW/alignment/Alignment.h:41:
291:info:build In file included from clustalW/alignment/Sequence.h:20:
292:info:build In file included from clustalW/alignment/../general/userparams.h:8:
293:info:build In file included from clustalW/general/UserParameters.h:22:
294:info:build In file included from clustalW/general/utils.h:8:
295:info:build In file included from clustalW/general/Utility.h:15:
296:info:build In file included from clustalW/general/clustalw.h:42:
297:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
298:info:build            int y = x.size();
299:info:build                ^
300:info:build In file included from AlignmentViewerWidget.cpp:66:
301:info:build In file included from ./AlignmentViewerWidget.h:36:
302:info:build In file included from ./clustalW/alignment/Alignment.h:41:
303:info:build In file included from clustalW/alignment/Sequence.h:20:
304:info:build In file included from clustalW/alignment/../general/userparams.h:8:
305:info:build In file included from clustalW/general/UserParameters.h:22:
306:info:build In file included from clustalW/general/utils.h:8:
307:info:build In file included from clustalW/general/Utility.h:15:
308:info:build In file included from clustalW/general/clustalw.h:43:
309:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
310:info:build            int y = x.size();
311:info:build                ^
312:info:build In file included from AlignmentWidget.cpp:49:
313:info:build In file included from ./AlignmentWidget.h:41:
314:info:build In file included from ./clustalW/alignment/Alignment.h:41:
315:info:build In file included from clustalW/alignment/Sequence.h:20:
316:info:build In file included from AlignmentFormatOptions.cpp:11:
317:info:build In file included from ./clustalW/general/userparams.h:8:
318:info:build In file included from clustalW/general/UserParameters.h:22:
319:info:build In file included from clustalW/general/utils.h:8:
320:info:build In file included from clustalW/general/Utility.h:15:
321:info:build In file included from clustalW/general/clustalw.h:42:
322:info:build clustalW/general/Array2D.h:28:16In file included from clustalW/alignment/../general/userparams.h:8:
323:info:build In file included from clustalW/general/UserParameters.h:22:
324:info:build In file included from clustalW/general/utils.h:8:
325:info:build In file included from clustalW/general/Utility.h:15:
326:info:build In file included from clustalW/general/clustalw.h:42:
327:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
328:info:build            int y = x.size();
329:info:build                ^
330:info:build : warning: unused variable 'y' [-Wunused-variable]
331:info:build            int y = x.size();
332:info:build                ^
333:info:build In file included from AlignmentWidget.cpp:49:
334:info:build In file included from ./AlignmentWidget.h:41:
335:info:build In file included from ./clustalW/alignment/Alignment.h:41:
336:info:build In file included from clustalW/alignment/Sequence.h:20:
337:info:build In file included from clustalW/alignment/../general/userparams.h:8:
338:info:build In file included from clustalW/general/UserParameters.h:22:
339:info:build In file included from clustalW/general/utils.h:8:
340:info:build In file included from clustalW/general/Utility.h:15:
341:info:build In file included from clustalW/general/clustalw.h:43:
342:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
343:info:build            int y = x.size();
344:info:build                ^
345:info:build In file included from AlignOutputFileNames.cpp:26:
346:info:build In file included from ./AlignOutputFileNames.h:10:
347:info:build In file included from ./ClustalQtParams.h:13:
348:info:build In file included from ./clustalW/alignment/Alignment.h:41:
349:info:build In file included from clustalW/alignment/Sequence.h:20:
350:info:build In file included from clustalW/alignment/../general/userparams.h:8:
351:info:build In file included from clustalW/general/UserParameters.h:22:
352:info:build In file included from clustalW/general/utils.h:8:
353:info:build In file included from clustalW/general/Utility.h:15:
354:info:build In file included from clustalW/general/clustalw.h:42:
355:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
356:info:build            int y = x.size();
357:info:build                ^
358:info:build In file included from AlignmentFormatOptions.cpp:11:
359:info:build In file included from ./clustalW/general/userparams.h:8:
360:info:build In file included from clustalW/general/UserParameters.h:22:
361:info:build In file included from clustalW/general/utils.h:8:
362:info:build In file included from clustalW/general/Utility.h:15:
363:info:build In file included from clustalW/general/clustalw.h:43:
364:info:build clustalW/general/SquareMat.h:26:16: warningIn file included from : unused variable 'y' [-Wunused-variable]
365:info:build AlignOutputFileNames.cpp:           int y = x.size();
366:info:build                ^
367:info:build 26:
368:info:build In file included from ./AlignOutputFileNames.h:10:
369:info:build In file included from ./ClustalQtParams.h:13:
370:info:build In file included from ./clustalW/alignment/Alignment.h:41:
371:info:build In file included from clustalW/alignment/Sequence.h:20:
372:info:build In file included from clustalW/alignment/../general/userparams.h:8:
373:info:build In file included from clustalW/general/UserParameters.h:22:
374:info:build In file included from clustalW/general/utils.h:8:
375:info:build In file included from clustalW/general/Utility.h:15:
376:info:build In file included from clustalW/general/clustalw.h:43:
377:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
378:info:build            int y = x.size();
379:info:build                ^
380:info:build In file included from ColorFileXmlParser.cpp:3:
381:info:build In file included from ./ColorFileXmlParser.h:9:
382:info:build In file included from ./ColorParameters.h:11:
383:info:build In file included from ./HardCodedColorScheme.h:8:
384:info:build In file included from ./ClustalQtParams.h:13:
385:info:build In file included from ./clustalW/alignment/Alignment.h:41:
386:info:build In file included from clustalW/alignment/Sequence.h:20:
387:info:build In file included from clustalW/alignment/../general/userparams.h:8:
388:info:build In file included from clustalW/general/UserParameters.h:22:
389:info:build In file included from clustalW/general/utils.h:8:
390:info:build In file included from clustalW/general/Utility.h:15:
391:info:build In file included from clustalW/general/clustalw.h:42:
392:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
393:info:build            int y = x.size();
394:info:build                ^
395:info:build In file included from AlignmentParameters.cpp:21:
396:info:build In file included from ./clustalW/general/userparams.h:8:
397:info:build In file included from clustalW/general/UserParameters.h:22:
398:info:build In file included from clustalW/general/utils.h:8:
399:info:build In file included from clustalW/general/Utility.h:15:
400:info:build In file included from clustalW/general/clustalw.h:42:
401:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
402:info:build            int y = x.size();
403:info:build                ^
404:info:build In file included from ColorFileXmlParser.cpp:3:
405:info:build In file included from ./ColorFileXmlParser.h:9:
406:info:build In file included from ./ColorParameters.h:11:
407:info:build In file included from ./HardCodedColorScheme.h:8:
408:info:build In file included from ./ClustalQtParams.h:13:
409:info:build In file included from ./clustalW/alignment/Alignment.h:41:
410:info:build In file included from clustalW/alignment/Sequence.h:20:
411:info:build In file included from clustalW/alignment/../general/userparams.h:8:
412:info:build In file included from clustalW/general/UserParameters.h:22:
413:info:build In file included from clustalW/general/utils.h:8:
414:info:build In file included from clustalW/general/Utility.h:15:
415:info:build In file included from clustalW/general/clustalw.h:43:
416:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
417:info:build            int y = x.size();
418:info:build                ^
419:info:build In file included from AlignmentParameters.cpp:21:
420:info:build In file included from ./clustalW/general/userparams.h:8:
421:info:build In file included from clustalW/general/UserParameters.h:22:
422:info:build In file included from clustalW/general/utils.h:8:
423:info:build In file included from clustalW/general/Utility.h:15:
424:info:build In file included from clustalW/general/clustalw.h:43:
425:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
426:info:build            int y = x.size();
427:info:build                ^
428:info:build In file included from BootstrapTreeDialog.cpp:18:
429:info:build In file included from ./BootstrapTreeDialog.h:11:
430:info:build In file included from ./ClustalQtParams.h:13:
431:info:build In file included from ./clustalW/alignment/Alignment.h:41:
432:info:build In file included from clustalW/alignment/Sequence.h:20:
433:info:build In file included from clustalW/alignment/../general/userparams.h:8:
434:info:build In file included from clustalW/general/UserParameters.h:22:
435:info:build In file included from clustalW/general/utils.h:8:
436:info:build In file included from clustalW/general/Utility.h:15:
437:info:build In file included from clustalW/general/clustalw.h:42:
438:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
439:info:build            int y = x.size();
440:info:build                ^
441:info:build In file included from BootstrapTreeDialog.cpp:18:
442:info:build In file included from ./BootstrapTreeDialog.h:11:
443:info:build In file included from ./ClustalQtParams.h:13:
444:info:build In file included from ./clustalW/alignment/Alignment.h:41:
445:info:build In file included from clustalW/alignment/Sequence.h:20:
446:info:build In file included from clustalW/alignment/../general/userparams.h:8:
447:info:build In file included from clustalW/general/UserParameters.h:22:
448:info:build In file included from clustalW/general/utils.h:8:
449:info:build In file included from clustalW/general/Utility.h:15:
450:info:build In file included from clustalW/general/clustalw.h:43:
451:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
452:info:build            int y = x.size();
453:info:build                ^
454:info:build In file included from AlignmentViewerWidget.cpp:66:
455:info:build In file included from ./AlignmentViewerWidget.h:36:
456:info:build In file included from ./clustalW/alignment/Alignment.h:42:
457:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
458:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
459:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
460:info:build                                                              ^
461:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
462:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
463:info:build                                                                  ^
464:info:build In file included from AlignOutputFileNames.cpp:26:
465:info:build In file included from ./AlignOutputFileNames.h:10:
466:info:build In file included from ./ClustalQtParams.h:13:
467:info:build In file included from ./clustalW/alignment/Alignment.h:42:
468:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
469:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
470:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
471:info:build                                                              ^
472:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
473:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
474:info:build                                                                  ^
475:info:build In file included from AlignmentWidget.cpp:49:
476:info:build In file included from ./AlignmentWidget.h:41:
477:info:build In file included from ./clustalW/alignment/Alignment.h:42:
478:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
479:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
480:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
481:info:build                                                              ^
482:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
483:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
484:info:build                                                                  ^
485:info:build In file included from AlignmentParameters.cpp:22:
486:info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8:
487:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
488:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
489:info:build                                                              ^
490:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
491:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
492:info:build                                                                  ^
493:info:build In file included from ColorFileXmlParser.cpp:3:
494:info:build In file included from ./ColorFileXmlParser.h:9:
495:info:build In file included from ./ColorParameters.h:11:
496:info:build In file included from ./HardCodedColorScheme.h:8:
497:info:build In file included from ./ClustalQtParams.h:13:
498:info:build In file included from ./clustalW/alignment/Alignment.h:42:
499:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
500:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
501:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
502:info:build                                                              ^
503:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
504:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
505:info:build                                                                  ^
506:info:build AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter]
507:info:build void AlignmentParameters::showEvent(QShowEvent* event)
508:info:build                                                 ^
509:info:build In file included from BootstrapTreeDialog.cpp:18:
510:info:build In file included from ./BootstrapTreeDialog.h:11:
511:info:build In file included from ./ClustalQtParams.h:13:
512:info:build In file included from ./clustalW/alignment/Alignment.h:42:
513:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
514:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
515:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
516:info:build                                                              ^
517:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
518:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
519:info:build                                                                  ^
520:info:build AlignmentWidget.cpp:67:7: warning: field 'blackAndWhite' will be initialized after field 'selectedColoredRes' [-Wreorder]
521:info:build       blackAndWhite(false),
522:info:build       ^
523:info:build ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter]
524:info:build                             QTreeWidgetItem *parentItem)
525:info:build                                              ^
526:info:build ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter]
527:info:build void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem)
528:info:build                                                                                      ^
529:info:build ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter]
530:info:build int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem)
531:info:build                                                                                     ^
532:info:build AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable]
533:info:build     int codeForSpace = clustalw::userParameters->resIndex(
534:info:build         ^
535:info:build AlignmentWidget.cpp:225:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
536:info:build         for(unsigned int j = 0; j < lengthLongestSeq; j++)
537:info:build                                 ~ ^ ~~~~~~~~~~~~~~~~
538:info:build AlignmentWidget.cpp:235:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
539:info:build                 if(code >= 0 && code < conservationPixmaps->size())
540:info:build                                 ~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
541:info:build AlignmentWidget.cpp:268:51: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
542:info:build                     if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size())
543:info:build                                         ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~
544:info:build AlignmentWidget.cpp:280:51: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
545:info:build                     if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size())
546:info:build                                         ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
547:info:build AlignmentWidget.cpp:291:86: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
548:info:build                     if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j)
549:info:build                                                                 ~~~~~~~~~~~~~~~~~~~~ ^ ~
550:info:build AlignmentWidget.cpp:333:14: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
551:info:build         if(i < secStructPixmaps->size() && i < secStructInfo.size())
552:info:build            ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~
553:info:build In file included from AlignmentFormatOptions.cpp:8:
554:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
555:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
556:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
557:info:build     char type;
558:info:build          ^
559:info:build In file included from AlignmentFormatOptions.cpp:11:
560:info:build In file included from ./clustalW/general/userparams.h:8:
561:info:build In file included from clustalW/general/UserParameters.h:22:
562:info:build In file included from clustalW/general/utils.h:8:
563:info:build In file included from clustalW/general/Utility.h:15:
564:info:build In file included from clustalW/general/clustalw.h:44:
565:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
566:info:build         int firstSeq, numSeqsInSub;
567:info:build             ^
568:info:build AlignmentWidget.cpp:569:36: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
569:info:build                     if(selectedRes >= selectedColoredRes->size())
570:info:build                        ~~~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~
571:info:build AlignmentWidget.cpp:689:30: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
572:info:build             for(int j = 1; j <= strongGroup.size(); j++)
573:info:build                            ~ ^  ~~~~~~~~~~~~~~~~~~
574:info:build AlignmentWidget.cpp:693:30: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
575:info:build             for(int j = 1; j <= weakGroup.size(); j++)
576:info:build                            ~ ^  ~~~~~~~~~~~~~~~~
577:info:build AlignmentWidget.cpp:700:35: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
578:info:build                 if((i + _fRes - 1 < (*alignment)[j].size()) &&
579:info:build                     ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~
580:info:build AlignmentWidget.cpp:701:35: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
581:info:build                    (i + _fRes - 1 < (*alignment)[_fSeq].size()))
582:info:build                     ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~
583:info:build AlignmentWidget.cpp:725:42: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
584:info:build                         for(int k = 1; k <= strongGroup.size(); k++)
585:info:build                                        ~ ^  ~~~~~~~~~~~~~~~~~~
586:info:build AlignmentWidget.cpp:737:42: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
587:info:build                         for(int k = 1; k <= weakGroup.size(); k++)
588:info:build                                        ~ ^  ~~~~~~~~~~~~~~~~
589:info:build AlignmentWidget.cpp:760:34: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
590:info:build                 for(int k = 1; k <= strongGroup.size(); k++)
591:info:build                                ~ ^  ~~~~~~~~~~~~~~~~~~
592:info:build AlignmentWidget.cpp:771:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
593:info:build                     for(int k = 1; k <= weakGroup.size(); k++)
594:info:build                                    ~ ^  ~~~~~~~~~~~~~~~~
595: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]
596:info:build             if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq))
597:info:build                ~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
598:info:build  warningAlignmentWidget.cpp:927:28: : comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
599:info:build             for(i = 0; i < len && i < gapMask->size(); i++)
600:info:build                                   ~ ^ ~~~~~~~~~~~~~~~
601:info:build AlignmentViewerWidget.cpp:645:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
602:info:build             for (i = 0; i < len && i < _secStructMask->size();i++)
603:info:build                                    ~ ^ ~~~~~~~~~~~~~~~~~~~~~~
604:info:build AlignmentViewerWidget.cpp:652:37: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
605:info:build             for(i = 0; i < len && i < ssMask.size(); i++)
606:info:build                                   ~ ^ ~~~~~~~~~~~~~
607:info:build warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
608:info:build                 if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq))
609:info:build                    ~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
610:info:build AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter]
611:info:build void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event )
612:info:build                                                          ^
613:info:build AlignmentWidget.cpp:1039:26: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
614:info:build         for(int j = 0; j < aminoAcid.size(); j++)
615:info:build                        ~ ^ ~~~~~~~~~~~~~~~~
616:info:build In file included from AlignmentParameters.cpp:14:
617:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
618:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
619:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
620:info:build     char type;
621:info:build          ^
622:info:build In file included from AlignmentParameters.cpp:21:
623:info:build In file included from ./clustalW/general/userparams.h:8:
624:info:build In file included from clustalW/general/UserParameters.h:22:
625:info:build In file included from clustalW/general/utils.h:8:
626:info:build In file included from clustalW/general/Utility.h:15:
627:info:build In file included from clustalW/general/clustalw.h:44:
628:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
629:info:build         int firstSeq, numSeqsInSub;
630:info:build             ^
631:info:build In file included from AlignOutputFileNames.cpp:23:
632:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
633:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
634:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
635:info:build     char type;
636:info:build          ^
637:info:build In file included from AlignOutputFileNames.cpp:26:
638:info:build In file included from ./AlignOutputFileNames.h:10:
639:info:build In file included from ./ClustalQtParams.h:13:
640:info:build In file included from ./clustalW/alignment/Alignment.h:41:
641:info:build In file included from clustalW/alignment/Sequence.h:20:
642:info:build In file included from clustalW/alignment/../general/userparams.h:8:
643:info:build In file included from clustalW/general/UserParameters.h:22:
644:info:build In file included from clustalW/general/utils.h:8:
645:info:build In file included from clustalW/general/Utility.h:15:
646:info:build In file included from clustalW/general/clustalw.h:44:
647:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
648:info:build         int firstSeq, numSeqsInSub;
649:info:build             ^
650:info:build In file included from ColorFileXmlParser.cpp:1:
651:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
652:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
653:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
654:info:build     char type;
655:info:build          ^
656:info:build In file included from ColorFileXmlParser.cpp:3:
657:info:build In file included from ./ColorFileXmlParser.h:9:
658:info:build In file included from ./ColorParameters.h:11:
659:info:build In file included from ./HardCodedColorScheme.h:8:
660:info:build In file included from ./ClustalQtParams.h:13:
661:info:build In file included from ./clustalW/alignment/Alignment.h:41:
662:info:build In file included from clustalW/alignment/Sequence.h:20:
663:info:build In file included from clustalW/alignment/../general/userparams.h:8:
664:info:build In file included from clustalW/general/UserParameters.h:22:
665:info:build In file included from clustalW/general/utils.h:8:
666:info:build In file included from clustalW/general/Utility.h:15:
667:info:build In file included from clustalW/general/clustalw.h:44:
668:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
669:info:build         int firstSeq, numSeqsInSub;
670:info:build             ^
671:info:build In file included from BootstrapTreeDialog.cpp:15:
672:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
673:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
674:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
675:info:build     char type;
676:info:build          ^
677:info:build In file included from BootstrapTreeDialog.cpp:18:
678:info:build In file included from ./BootstrapTreeDialog.h:11:
679:info:build In file included from ./ClustalQtParams.h:13:
680:info:build In file included from ./clustalW/alignment/Alignment.h:41:
681:info:build In file included from clustalW/alignment/Sequence.h:20:
682:info:build In file included from clustalW/alignment/../general/userparams.h:8:
683:info:build In file included from clustalW/general/UserParameters.h:22:
684:info:build In file included from clustalW/general/utils.h:8:
685:info:build In file included from clustalW/general/Utility.h:15:
686:info:build In file included from clustalW/general/clustalw.h:44:
687:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
688:info:build         int firstSeq, numSeqsInSub;
689:info:build             ^
690:info:build 4 warnings generated.
691: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
692:info:build In file included from AlignmentViewerWidget.cpp:63:
693:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
694:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
695:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
696:info:build     char type;
697:info:build          ^
698:info:build In file included from AlignmentViewerWidget.cpp:66:
699:info:build In file included from ./AlignmentViewerWidget.h:36:
700:info:build In file included from ./clustalW/alignment/Alignment.h:41:
701:info:build In file included from clustalW/alignment/Sequence.h:20:
702:info:build In file included from clustalW/alignment/../general/userparams.h:8:
703:info:build In file included from clustalW/general/UserParameters.h:22:
704:info:build In file included from clustalW/general/utils.h:8:
705:info:build In file included from clustalW/general/Utility.h:15:
706:info:build In file included from clustalW/general/clustalw.h:44:
707:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
708:info:build         int firstSeq, numSeqsInSub;
709:info:build             ^
710:info:build In file included from AlignmentWidget.cpp:48:
711:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
712:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
713:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
714:info:build     char type;
715:info:build          ^
716:info:build In file included from AlignmentWidget.cpp:49:
717:info:build In file included from ./AlignmentWidget.h:41:
718:info:build In file included from ./clustalW/alignment/Alignment.h:41:
719:info:build In file included from clustalW/alignment/Sequence.h:20:
720:info:build In file included from clustalW/alignment/../general/userparams.h:8:
721:info:build In file included from clustalW/general/UserParameters.h:22:
722:info:build In file included from clustalW/general/utils.h:8:
723:info:build In file included from clustalW/general/Utility.h:15:
724:info:build In file included from clustalW/general/clustalw.h:44:
725:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
726:info:build         int firstSeq, numSeqsInSub;
727:info:build             ^
728:info:build 7 warnings generated.
729: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
730:info:build 6 warnings generated.
731: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
732:info:build 9 warnings generated.
733: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
734:info:build 6 warnings generated.
735: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
736: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
737:info:build 10 warnings generated.
738: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
739:info:build In file included from HardCodedColorScheme.cpp:1:
740:info:build In file included from ./HardCodedColorScheme.h:8:
741:info:build In file included from ./ClustalQtParams.h:13:
742:info:build In file included from ./clustalW/alignment/Alignment.h:41:
743:info:build In file included from clustalW/alignment/Sequence.h:20:
744:info:build In file included from clustalW/alignment/../general/userparams.h:8:
745:info:build In file included from clustalW/general/UserParameters.h:22:
746:info:build In file included from clustalW/general/utils.h:8:
747:info:build In file included from clustalW/general/Utility.h:15:
748:info:build In file included from clustalW/general/clustalw.h:42:
749:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
750:info:build            int y = x.size();
751:info:build                ^
752:info:build In file included from HardCodedColorScheme.cpp:1:
753:info:build In file included from ./HardCodedColorScheme.h:8:
754:info:build In file included from ./ClustalQtParams.h:13:
755:info:build In file included from ./clustalW/alignment/Alignment.h:41:
756:info:build In file included from clustalW/alignment/Sequence.h:20:
757:info:build In file included from clustalW/alignment/../general/userparams.h:8:
758:info:build In file included from clustalW/general/UserParameters.h:22:
759:info:build In file included from clustalW/general/utils.h:8:
760:info:build In file included from clustalW/general/Utility.h:15:
761:info:build In file included from clustalW/general/clustalw.h:43:
762:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
763:info:build            int y = x.size();
764:info:build                ^
765:info:build In file included from HardCodedColorScheme.cpp:1:
766:info:build In file included from ./HardCodedColorScheme.h:8:
767:info:build In file included from ./ClustalQtParams.h:13:
768:info:build In file included from ./clustalW/alignment/Alignment.h:42:
769:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
770:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
771:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
772:info:build                                                              ^
773:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
774:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
775:info:build                                                                  ^
776:info:build In file included from HelpDisplayWidget.cpp:15:
777:info:build In file included from ./HelpDisplayWidget.h:17:
778:info:build In file included from ./clustalW/general/clustalw.h:42:
779:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
780:info:build            int y = x.size();
781:info:build                ^
782:info:build In file included from HelpDisplayWidget.cpp:15:
783:info:build In file included from ./HelpDisplayWidget.h:17:
784:info:build In file included from ./clustalW/general/clustalw.h:43:
785:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
786:info:build            int y = x.size();
787:info:build                ^
788:info:build In file included from HardCodedColorScheme.cpp:1:
789:info:build In file included from ./HardCodedColorScheme.h:8:
790:info:build In file included from ./ClustalQtParams.h:13:
791:info:build In file included from ./clustalW/alignment/Alignment.h:41:
792:info:build In file included from clustalW/alignment/Sequence.h:20:
793:info:build In file included from clustalW/alignment/../general/userparams.h:8:
794:info:build In file included from clustalW/general/UserParameters.h:22:
795:info:build In file included from clustalW/general/utils.h:8:
796:info:build In file included from clustalW/general/Utility.h:15:
797:info:build In file included from clustalW/general/clustalw.h:44:
798:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
799:info:build         int firstSeq, numSeqsInSub;
800:info:build             ^
801:info:build In file included from KeyController.cpp:9:
802:info:build In file included from ./KeyController.h:13:
803:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QKeyEvent:1:
804:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
805:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
806:info:build     char type;
807:info:build          ^
808:info:build 1 warning generated.
809: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
810:info:build In file included from ColumnScoreParams.cpp:22:
811:info:build In file included from ./clustalW/general/userparams.h:8:
812:info:build In file included from clustalW/general/UserParameters.h:22:
813:info:build In file included from clustalW/general/utils.h:8:
814:info:build In file included from clustalW/general/Utility.h:15:
815:info:build In file included from clustalW/general/clustalw.h:42:
816:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
817:info:build            int y = x.size();
818:info:build                ^
819:info:build In file included from HelpDisplayWidget.cpp:15:
820:info:build In file included from ./HelpDisplayWidget.h:18:
821:info:build In file included from ./ClustalQtParams.h:13:
822:info:build In file included from ./clustalW/alignment/Alignment.h:42:
823:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
824:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
825:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
826:info:build                                                              ^
827:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
828:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
829:info:build                                                                  ^
830:info:build In file included from ColumnScoreParams.cpp:22:
831:info:build In file included from ./clustalW/general/userparams.h:8:
832:info:build In file included from clustalW/general/UserParameters.h:22:
833:info:build In file included from clustalW/general/utils.h:8:
834:info:build In file included from clustalW/general/Utility.h:15:
835:info:build In file included from clustalW/general/clustalw.h:43:
836:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
837:info:build            int y = x.size();
838:info:build                ^
839:info:build 5 warnings generated.
840: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
841:info:build 26 warnings generated.
842: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
843:info:build In file included from ColumnScoreParams.cpp:23:
844:info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8:
845:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
846:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
847:info:build                                                              ^
848:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
849:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
850:info:build                                                                  ^
851:info:build ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter]
852:info:build void ColumnScoreParams::showEvent(QShowEvent* event)
853:info:build                                               ^
854:info:build In file included from ColumnScoreParams.cpp:14:
855:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
856:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
857:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
858:info:build     char type;
859:info:build          ^
860:info:build In file included from ColumnScoreParams.cpp:22:
861:info:build In file included from ./clustalW/general/userparams.h:8:
862:info:build In file included from clustalW/general/UserParameters.h:22:
863:info:build In file included from clustalW/general/utils.h:8:
864:info:build In file included from clustalW/general/Utility.h:15:
865:info:build In file included from clustalW/general/clustalw.h:44:
866:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
867:info:build         int firstSeq, numSeqsInSub;
868:info:build             ^
869:info:build 7 warnings generated.
870: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
871:info:build In file included from main.cpp:21:
872:info:build In file included from ./clustalW/substitutionMatrix/SubMatrix.h:28:
873:info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:42:
874:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
875:info:build            int y = x.size();
876:info:build                ^
877:info:build In file included from main.cpp:21:
878:info:build In file included from ./clustalW/substitutionMatrix/SubMatrix.h:28:
879:info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:43:
880:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
881:info:build            int y = x.size();
882:info:build                ^
883:info:build In file included from main.cpp:21:
884:info:build ./clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
885:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
886:info:build                                                              ^
887:info:build ./clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
888:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
889:info:build                                                                  ^
890:info:build In file included from main.cpp:22:
891:info:build ./QTUtility.h:28:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual]
892:info:build         virtual char promptForYesNo(char *title,char *prompt);
893:info:build                      ^
894: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 *')
895:info:build         virtual char promptForYesNo(char *title, const char *prompt);
896:info:build                      ^
897: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 *')
898:info:build         virtual char promptForYesNo(const char *title, const char *prompt);
899:info:build                      ^
900:info:build In file included from main.cpp:22:
901:info:build ./QTUtility.h:29:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual]
902:info:build         virtual char promptForYesNo(const char *title,char *prompt);
903:info:build                      ^
904: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 *')
905:info:build         virtual char promptForYesNo(char *title, const char *prompt);
906:info:build                      ^
907: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 *')
908:info:build         virtual char promptForYesNo(const char *title, const char *prompt);
909:info:build                      ^
910:info:build In file included from PostscriptFileParams.cpp:1:
911:info:build In file included from ./PostscriptFileParams.h:4:
912:info:build In file included from ./ClustalQtParams.h:13:
913:info:build In file included from ./clustalW/alignment/Alignment.h:41:
914:info:build In file included from clustalW/alignment/Sequence.h:20:
915:info:build In file included from clustalW/alignment/../general/userparams.h:8:
916:info:build In file included from clustalW/general/UserParameters.h:22:
917:info:build In file included from clustalW/general/utils.h:8:
918:info:build In file included from clustalW/general/Utility.h:15:
919:info:build In file included from clustalW/general/clustalw.h:42:
920:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
921:info:build            int y = x.size();
922:info:build                ^
923:info:build In file included from PostscriptFileParams.cpp:1:
924:info:build In file included from ./PostscriptFileParams.h:4:
925:info:build In file included from ./ClustalQtParams.h:13:
926:info:build In file included from ./clustalW/alignment/Alignment.h:41:
927:info:build In file included from clustalW/alignment/Sequence.h:20:
928:info:build In file included from clustalW/alignment/../general/userparams.h:8:
929:info:build In file included from clustalW/general/UserParameters.h:22:
930:info:build In file included from clustalW/general/utils.h:8:
931:info:build In file included from clustalW/general/Utility.h:15:
932:info:build In file included from clustalW/general/clustalw.h:43:
933:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
934:info:build            int y = x.size();
935:info:build                ^
936:info:build In file included from PostscriptFileParams.cpp:1:
937:info:build In file included from ./PostscriptFileParams.h:4:
938:info:build In file included from ./ClustalQtParams.h:13:
939:info:build In file included from ./clustalW/alignment/Alignment.h:42:
940:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
941:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
942:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
943:info:build                                                              ^
944:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
945:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
946:info:build                                                                  ^
947:info:build In file included from PostscriptFileParams.cpp:1:
948:info:build In file included from ./PostscriptFileParams.h:4:
949:info:build In file included from ./ClustalQtParams.h:13:
950:info:build In file included from ./clustalW/alignment/Alignment.h:41:
951:info:build In file included from clustalW/alignment/Sequence.h:20:
952:info:build In file included from clustalW/alignment/../general/userparams.h:8:
953:info:build In file included from clustalW/general/UserParameters.h:22:
954:info:build In file included from clustalW/general/utils.h:8:
955:info:build In file included from clustalW/general/Utility.h:15:
956:info:build In file included from clustalW/general/clustalw.h:44:
957:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
958:info:build         int firstSeq, numSeqsInSub;
959:info:build             ^
960:info:build 5 warnings generated.
961: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
962:info:build HistogramWidget.cpp:180:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
963:info:build             if(column >= 0 && column < arrayOfHeights->size())
964:info:build                               ~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~
965:info:build HistogramWidget.cpp:198:38: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
966:info:build             if(column >= 0 && column < arrayOfHeights->size())
967:info:build                               ~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~
968:info:build In file included from HistogramWidget.cpp:24:
969:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
970:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
971:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
972:info:build     char type;
973:info:build          ^
974:info:build 3 warnings generated.
975: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
976:info:build In file included from main.cpp:21:
977:info:build In file included from ./clustalW/substitutionMatrix/SubMatrix.h:28:
978:info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:44:
979:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
980:info:build         int firstSeq, numSeqsInSub;
981:info:build             ^
982:info:build In file included from main.cpp:24:
983:info:build In file included from ./mainwindow.h:37:
984:info:build In file included from ./AlignmentViewerWidget.h:37:
985:info:build In file included from ./AlignmentWidget.h:43:
986:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QKeyEvent:1:
987:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
988:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
989:info:build     char type;
990:info:build          ^
991:info:build 8 warnings generated.
992: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
993:info:build In file included from HelpDisplayWidget.cpp:15:
994:info:build In file included from ./HelpDisplayWidget.h:17:
995:info:build In file included from ./clustalW/general/clustalw.h:44:
996:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
997:info:build         int firstSeq, numSeqsInSub;
998:info:build             ^
999:info:build In file included from HelpDisplayWidget.cpp:19:
1000:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1001:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1002:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1003:info:build     char type;
1004:info:build          ^
1005:info:build In file included from LowScoringSegParams.cpp:22:
1006:info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8:
1007:info:build In file included from clustalW/substitutionMatrix/SubMatrix.h:28:
1008:info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:42:
1009:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1010:info:build            int y = x.size();
1011:info:build                ^
1012:info:build In file included from LowScoringSegParams.cpp:22:
1013:info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8:
1014:info:build In file included from clustalW/substitutionMatrix/SubMatrix.h:28:
1015:info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:43:
1016:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1017:info:build            int y = x.size();
1018:info:build                ^
1019:info:build 6 warnings generated.
1020: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
1021:info:build In file included from LowScoringSegParams.cpp:22:
1022:info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8:
1023:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1024:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1025:info:build                                                              ^
1026:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1027:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1028:info:build                                                                  ^
1029:info:build LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter]
1030:info:build void LowScoringSegParams::showEvent(QShowEvent* event)
1031:info:build                                                 ^
1032:info:build In file included from LowScoringSegParams.cpp:15:
1033:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1034:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1035:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1036:info:build     char type;
1037:info:build          ^
1038:info:build In file included from LowScoringSegParams.cpp:22:
1039:info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8:
1040:info:build In file included from clustalW/substitutionMatrix/SubMatrix.h:28:
1041:info:build In file included from clustalW/substitutionMatrix/../general/clustalw.h:44:
1042:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1043:info:build         int firstSeq, numSeqsInSub;
1044:info:build             ^
1045:info:build 7 warnings generated.
1046: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
1047:info:build In file included from mainwindow.cpp:98:
1048:info:build In file included from ./mainwindow.h:37:
1049:info:build In file included from ./AlignmentViewerWidget.h:36:
1050:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1051:info:build In file included from clustalW/alignment/Sequence.h:20:
1052:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1053:info:build In file included from clustalW/general/UserParameters.h:22:
1054:info:build In file included from clustalW/general/utils.h:8:
1055:info:build In file included from clustalW/general/Utility.h:15:
1056:info:build In file included from clustalW/general/clustalw.h:42:
1057:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1058:info:build            int y = x.size();
1059:info:build                ^
1060:info:build In file included from mainwindow.cpp:98:
1061:info:build In file included from ./mainwindow.h:37:
1062:info:build In file included from ./AlignmentViewerWidget.h:36:
1063:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1064:info:build In file included from clustalW/alignment/Sequence.h:20:
1065:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1066:info:build In file included from clustalW/general/UserParameters.h:22:
1067:info:build In file included from clustalW/general/utils.h:8:
1068:info:build In file included from clustalW/general/Utility.h:15:
1069:info:build In file included from clustalW/general/clustalw.h:43:
1070:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1071:info:build            int y = x.size();
1072:info:build                ^
1073:info:build In file included from QTUtility.cpp:7:
1074:info:build In file included from ./QTUtility.h:11:
1075:info:build In file included from ./clustalW/general/clustalw.h:42:
1076:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1077:info:build            int y = x.size();
1078:info:build                ^
1079:info:build In file included from QTUtility.cpp:7:
1080:info:build In file included from ./QTUtility.h:11:
1081:info:build In file included from ./clustalW/general/clustalw.h:43:
1082:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1083:info:build            int y = x.size();
1084:info:build                ^
1085:info:build In file included from PairwiseParams.cpp:22:
1086:info:build In file included from ./clustalW/general/userparams.h:8:
1087:info:build In file included from clustalW/general/UserParameters.h:22:
1088:info:build In file included from clustalW/general/utils.h:8:
1089:info:build In file included from clustalW/general/Utility.h:15:
1090:info:build In file included from clustalW/general/clustalw.h:42:
1091:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1092:info:build            int y = x.size();
1093:info:build                ^
1094:info:build In file included from PairwiseParams.cpp:22:
1095:info:build In file included from ./clustalW/general/userparams.h:8:
1096:info:build In file included from clustalW/general/UserParameters.h:22:
1097:info:build In file included from clustalW/general/utils.h:8:
1098:info:build In file included from clustalW/general/Utility.h:15:
1099:info:build In file included from clustalW/general/clustalw.h:43:
1100:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1101:info:build            int y = x.size();
1102:info:build                ^
1103:info:build In file included from mainwindow.cpp:98:
1104:info:build In file included from ./mainwindow.h:37:
1105:info:build In file included from ./AlignmentViewerWidget.h:36:
1106:info:build In file included from ./clustalW/alignment/Alignment.h:42:
1107:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1108:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1109:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1110:info:build                                                              ^
1111:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1112:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1113:info:build                                                                  ^
1114:info:build In file included from QTUtility.cpp:7:
1115:info:build ./QTUtility.h:28:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual]
1116:info:build         virtual char promptForYesNo(char *title,char *prompt);
1117:info:build                      ^
1118: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 *')
1119:info:build         virtual char promptForYesNo(char *title, const char *prompt);
1120:info:build                      ^
1121: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 *')
1122:info:build         virtual char promptForYesNo(const char *title, const char *prompt);
1123:info:build                      ^
1124:info:build In file included from QTUtility.cpp:7:
1125:info:build ./QTUtility.h:29:22: warning: 'clustalw::QTUtility::promptForYesNo' hides overloaded virtual functions [-Woverloaded-virtual]
1126:info:build         virtual char promptForYesNo(const char *title,char *prompt);
1127:info:build                      ^
1128: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 *')
1129:info:build         virtual char promptForYesNo(char *title, const char *prompt);
1130:info:build                      ^
1131: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 *')
1132:info:build         virtual char promptForYesNo(const char *title, const char *prompt);
1133:info:build                      ^
1134: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
1135:info:build In file included from PairwiseParams.cpp:23:
1136:info:build In file included from ./clustalW/substitutionMatrix/globalmatrix.h:8:
1137:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1138:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1139:info:build                                                              ^
1140:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1141:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1142:info:build                                                                  ^
1143:info:build In file included from QTUtility.cpp:7:
1144:info:build In file included from ./QTUtility.h:11:
1145:info:build In file included from ./clustalW/general/clustalw.h:44:
1146:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1147:info:build         int firstSeq, numSeqsInSub;
1148:info:build             ^
1149:info:build PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter]
1150:info:build void PairwiseParams::showEvent(QShowEvent* event)
1151:info:build                                            ^
1152:info:build mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter]
1153:info:build void MainWindow::showEvent(QShowEvent* event)
1154:info:build                                        ^
1155:info:build In file included from PairwiseParams.cpp:21:
1156:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1157:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1158:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1159:info:build     char type;
1160:info:build          ^
1161:info:build In file included from PairwiseParams.cpp:22:
1162:info:build In file included from ./clustalW/general/userparams.h:8:
1163:info:build In file included from clustalW/general/UserParameters.h:22:
1164:info:build In file included from clustalW/general/utils.h:8:
1165:info:build In file included from clustalW/general/Utility.h:15:
1166:info:build In file included from clustalW/general/clustalw.h:44:
1167:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1168:info:build         int firstSeq, numSeqsInSub;
1169:info:build             ^
1170:info:build 5 warnings generated.
1171: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
1172:info:build mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter]
1173:info:build void MainWindow::writeViewer1AsPostscript(int type)
1174:info:build                                               ^
1175:info:build In file included from ProteinGapParameters.cpp:13:
1176:info:build In file included from ./clustalW/general/userparams.h:8:
1177:info:build In file included from clustalW/general/UserParameters.h:22:
1178:info:build In file included from clustalW/general/utils.h:8:
1179:info:build In file included from clustalW/general/Utility.h:15:
1180:info:build In file included from clustalW/general/clustalw.h:42:
1181:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1182:info:build            int y = x.size();
1183:info:build                ^
1184:info:build In file included from ProteinGapParameters.cpp:13:
1185:info:build In file included from ./clustalW/general/userparams.h:8:
1186:info:build In file included from clustalW/general/UserParameters.h:22:
1187:info:build In file included from clustalW/general/utils.h:8:
1188:info:build In file included from clustalW/general/Utility.h:15:
1189:info:build In file included from clustalW/general/clustalw.h:43:
1190:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1191:info:build            int y = x.size();
1192:info:build                ^
1193:info:build 7 warnings generated.
1194: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
1195:info:build In file included from mainwindow.cpp:90:
1196:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1197:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1198:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1199:info:build     char type;
1200:info:build          ^
1201:info:build In file included from mainwindow.cpp:98:
1202:info:build In file included from ./mainwindow.h:37:
1203:info:build In file included from ./AlignmentViewerWidget.h:36:
1204:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1205:info:build In file included from clustalW/alignment/Sequence.h:20:
1206:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1207:info:build In file included from clustalW/general/UserParameters.h:22:
1208:info:build In file included from clustalW/general/utils.h:8:
1209:info:build In file included from clustalW/general/Utility.h:15:
1210:info:build In file included from clustalW/general/clustalw.h:44:
1211:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1212:info:build         int firstSeq, numSeqsInSub;
1213:info:build             ^
1214:info:build In file included from ProteinGapParameters.cpp:8:
1215:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1216:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1217:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1218:info:build     char type;
1219:info:build          ^
1220:info:build In file included from ProteinGapParameters.cpp:13:
1221:info:build In file included from ./clustalW/general/userparams.h:8:
1222:info:build In file included from clustalW/general/UserParameters.h:22:
1223:info:build In file included from clustalW/general/utils.h:8:
1224:info:build In file included from clustalW/general/Utility.h:15:
1225:info:build In file included from clustalW/general/clustalw.h:44:
1226:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1227:info:build         int firstSeq, numSeqsInSub;
1228:info:build             ^
1229:info:build 4 warnings generated.
1230: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
1231: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
1232:info:build In file included from PSPrinter.cpp:20:
1233:info:build In file included from ./PSPrinter.h:11:
1234:info:build In file included from ./ColorParameters.h:11:
1235:info:build In file included from ./HardCodedColorScheme.h:8:
1236:info:build In file included from ./ClustalQtParams.h:13:
1237:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1238:info:build In file included from clustalW/alignment/Sequence.h:20:
1239:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1240:info:build In file included from clustalW/general/UserParameters.h:22:
1241:info:build In file included from clustalW/general/utils.h:8:
1242:info:build In file included from clustalW/general/Utility.h:15:
1243:info:build In file included from clustalW/general/clustalw.h:42:
1244:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1245:info:build            int y = x.size();
1246:info:build                ^
1247:info:build In file included from PSPrinter.cpp:20:
1248:info:build In file included from ./PSPrinter.h:11:
1249:info:build In file included from ./ColorParameters.h:11:
1250:info:build In file included from ./HardCodedColorScheme.h:8:
1251:info:build In file included from ./ClustalQtParams.h:13:
1252:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1253:info:build In file included from clustalW/alignment/Sequence.h:20:
1254:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1255:info:build In file included from clustalW/general/UserParameters.h:22:
1256:info:build In file included from clustalW/general/utils.h:8:
1257:info:build In file included from clustalW/general/Utility.h:15:
1258:info:build In file included from clustalW/general/clustalw.h:43:
1259:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1260:info:build            int y = x.size();
1261:info:build                ^
1262:info:build In file included from PSPrinter.cpp:20:
1263:info:build In file included from ./PSPrinter.h:11:
1264:info:build In file included from ./ColorParameters.h:11:
1265:info:build In file included from ./HardCodedColorScheme.h:8:
1266:info:build In file included from ./ClustalQtParams.h:13:
1267:info:build In file included from ./clustalW/alignment/Alignment.h:42:
1268:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1269:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1270:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1271:info:build                                                              ^
1272:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1273:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1274:info:build                                                                  ^
1275:info:build PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable]
1276:info:build     int err;
1277:info:build         ^
1278:info:build PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable]
1279:info:build     int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local
1280:info:build         ^
1281:info:build PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable]
1282:info:build     int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local
1283:info:build         ^
1284:info:build PSPrinter.cpp:207:55: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare]
1285:info:build                 if(res.isLetter() && resNumber.size() > i - data->firstSeq)
1286:info:build                                      ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~
1287:info:build PSPrinter.cpp:307:67: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare]
1288:info:build                             if(res.isLetter() && resNumber.size() > seq)
1289:info:build                                                  ~~~~~~~~~~~~~~~~ ^ ~~~
1290:info:build PSPrinter.cpp:421:67: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare]
1291:info:build                             if(res.isLetter() && resNumber.size() > i)
1292:info:build                                                  ~~~~~~~~~~~~~~~~ ^ ~
1293:info:build PSPrinter.cpp:587:32: warning: comparison of integers of different signs: 'size_type' (aka 'unsigned long') and 'int' [-Wsign-compare]
1294:info:build     if(data->nameHeader.size() > ix)
1295:info:build        ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~
1296:info:build PSPrinter.cpp:730:30: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
1297:info:build     for(i = fr; i <= lr && i < ruler.length(); i++)
1298:info:build                            ~ ^ ~~~~~~~~~~~~~~
1299:info:build PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable]
1300:info:build     int psX, psY, curveBottom;
1301:info:build              ^
1302:info:build PSPrinter.cpp:789:34: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
1303:info:build     for(i = fr + 1; i <= lr && i < data->histogram->size(); i++)
1304:info:build                                ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~
1305:info:build In file included from PSPrinter.cpp:19:
1306:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1307:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1308:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1309:info:build     char type;
1310:info:build          ^
1311:info:build In file included from PSPrinter.cpp:20:
1312:info:build In file included from ./PSPrinter.h:11:
1313:info:build In file included from ./ColorParameters.h:11:
1314:info:build In file included from ./HardCodedColorScheme.h:8:
1315:info:build In file included from ./ClustalQtParams.h:13:
1316:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1317:info:build In file included from clustalW/alignment/Sequence.h:20:
1318:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1319:info:build In file included from clustalW/general/UserParameters.h:22:
1320:info:build In file included from clustalW/general/utils.h:8:
1321:info:build In file included from clustalW/general/Utility.h:15:
1322:info:build In file included from clustalW/general/clustalw.h:44:
1323:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1324:info:build         int firstSeq, numSeqsInSub;
1325:info:build             ^
1326:info:build In file included from SaveSeqFile.cpp:23:
1327:info:build In file included from ./SaveSeqFile.h:9:
1328:info:build In file included from ./ClustalQtParams.h:13:
1329:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1330:info:build In file included from clustalW/alignment/Sequence.h:20:
1331:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1332:info:build In file included from clustalW/general/UserParameters.h:22:
1333:info:build In file included from clustalW/general/utils.h:8:
1334:info:build In file included from clustalW/general/Utility.h:15:
1335:info:build In file included from clustalW/general/clustalw.h:42:
1336:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1337:info:build            int y = x.size();
1338:info:build                ^
1339:info:build In file included from SaveSeqFile.cpp:23:
1340:info:build In file included from ./SaveSeqFile.h:9:
1341:info:build In file included from ./ClustalQtParams.h:13:
1342:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1343:info:build In file included from clustalW/alignment/Sequence.h:20:
1344:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1345:info:build In file included from clustalW/general/UserParameters.h:22:
1346:info:build In file included from clustalW/general/utils.h:8:
1347:info:build In file included from clustalW/general/Utility.h:15:
1348:info:build In file included from clustalW/general/clustalw.h:43:
1349:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1350:info:build            int y = x.size();
1351:info:build                ^
1352:info:build In file included from SaveSeqFile.cpp:23:
1353:info:build In file included from ./SaveSeqFile.h:9:
1354:info:build In file included from ./ClustalQtParams.h:13:
1355:info:build In file included from ./clustalW/alignment/Alignment.h:42:
1356:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1357:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1358:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1359:info:build                                                              ^
1360:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1361:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1362:info:build                                                                  ^
1363:info:build In file included from SaveSeqFile.cpp:21:
1364:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1365:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1366:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1367:info:build     char type;
1368:info:build          ^
1369:info:build In file included from SaveSeqFile.cpp:23:
1370:info:build In file included from ./SaveSeqFile.h:9:
1371:info:build In file included from ./ClustalQtParams.h:13:
1372:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1373:info:build In file included from clustalW/alignment/Sequence.h:20:
1374:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1375:info:build In file included from clustalW/general/UserParameters.h:22:
1376:info:build In file included from clustalW/general/utils.h:8:
1377:info:build In file included from clustalW/general/Utility.h:15:
1378:info:build In file included from clustalW/general/clustalw.h:44:
1379:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1380:info:build         int firstSeq, numSeqsInSub;
1381:info:build             ^
1382:info:build 16 warnings generated.
1383: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
1384:info:build 6 warnings generated.
1385: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
1386:info:build In file included from SecStructOptions.cpp:12:
1387:info:build In file included from ./clustalW/general/userparams.h:8:
1388:info:build In file included from clustalW/general/UserParameters.h:22:
1389:info:build In file included from clustalW/general/utils.h:8:
1390:info:build In file included from clustalW/general/Utility.h:15:
1391:info:build In file included from clustalW/general/clustalw.h:42:
1392:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1393:info:build            int y = x.size();
1394:info:build                ^
1395:info:build In file included from SecStructOptions.cpp:12:
1396:info:build In file included from ./clustalW/general/userparams.h:8:
1397:info:build In file included from clustalW/general/UserParameters.h:22:
1398:info:build In file included from clustalW/general/utils.h:8:
1399:info:build In file included from clustalW/general/Utility.h:15:
1400:info:build In file included from clustalW/general/clustalw.h:43:
1401:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1402:info:build            int y = x.size();
1403:info:build                ^
1404:info:build In file included from SeqNameWidget.cpp:59:
1405:info:build In file included from ./SeqNameWidget.h:41:
1406:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1407:info:build In file included from clustalW/alignment/Sequence.h:20:
1408:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1409:info:build In file included from clustalW/general/UserParameters.h:22:
1410:info:build In file included from clustalW/general/utils.h:8:
1411:info:build In file included from clustalW/general/Utility.h:15:
1412:info:build In file included from clustalW/general/clustalw.h:42:
1413:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1414:info:build            int y = x.size();
1415:info:build                ^
1416:info:build In file included from SeqNameWidget.cpp:59:
1417:info:build In file included from ./SeqNameWidget.h:41:
1418:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1419:info:build In file included from clustalW/alignment/Sequence.h:20:
1420:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1421:info:build In file included from clustalW/general/UserParameters.h:22:
1422:info:build In file included from clustalW/general/utils.h:8:
1423:info:build In file included from clustalW/general/Utility.h:15:
1424:info:build In file included from clustalW/general/clustalw.h:43:
1425:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1426:info:build            int y = x.size();
1427:info:build                ^
1428:info:build In file included from SecStructOptions.cpp:8:
1429:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1430:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1431:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1432:info:build     char type;
1433:info:build          ^
1434:info:build In file included from SecStructOptions.cpp:12:
1435:info:build In file included from ./clustalW/general/userparams.h:8:
1436:info:build In file included from clustalW/general/UserParameters.h:22:
1437:info:build In file included from clustalW/general/utils.h:8:
1438:info:build In file included from clustalW/general/Utility.h:15:
1439:info:build In file included from clustalW/general/clustalw.h:44:
1440:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1441:info:build         int firstSeq, numSeqsInSub;
1442:info:build             ^
1443:info:build In file included from SeqNameWidget.cpp:59:
1444:info:build In file included from ./SeqNameWidget.h:41:
1445:info:build In file included from ./clustalW/alignment/Alignment.h:42:
1446:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1447:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1448:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1449:info:build                                                              ^
1450:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1451:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1452:info:build                                                                  ^
1453:info:build SeqNameWidget.cpp:375:11: warning: unused variable 'redrawRect' [-Wunused-variable]
1454:info:build     QRect redrawRect = event->rect();
1455:info:build           ^
1456:info:build 4 warnings generated.
1457: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
1458:info:build In file included from TreeFormatOptions.cpp:11:
1459:info:build In file included from ./clustalW/general/userparams.h:8:
1460:info:build In file included from clustalW/general/UserParameters.h:22:
1461:info:build In file included from clustalW/general/utils.h:8:
1462:info:build In file included from clustalW/general/Utility.h:15:
1463:info:build In file included from clustalW/general/clustalw.h:42:
1464:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1465:info:build            int y = x.size();
1466:info:build                ^
1467:info:build In file included from TreeFormatOptions.cpp:11:
1468:info:build In file included from ./clustalW/general/userparams.h:8:
1469:info:build In file included from clustalW/general/UserParameters.h:22:
1470:info:build In file included from clustalW/general/utils.h:8:
1471:info:build In file included from clustalW/general/Utility.h:15:
1472:info:build In file included from clustalW/general/clustalw.h:43:
1473:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1474:info:build            int y = x.size();
1475:info:build                ^
1476:info:build 8 warnings generated.
1477: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
1478:info:build In file included from SeqNameWidget.cpp:58:
1479:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1480:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1481:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1482:info:build     char type;
1483:info:build          ^
1484:info:build In file included from SeqNameWidget.cpp:59:
1485:info:build In file included from ./SeqNameWidget.h:41:
1486:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1487:info:build In file included from clustalW/alignment/Sequence.h:20:
1488:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1489:info:build In file included from clustalW/general/UserParameters.h:22:
1490:info:build In file included from clustalW/general/utils.h:8:
1491:info:build In file included from clustalW/general/Utility.h:15:
1492:info:build In file included from clustalW/general/clustalw.h:44:
1493:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1494:info:build         int firstSeq, numSeqsInSub;
1495:info:build             ^
1496:info:build In file included from clustalW/Clustal.cpp:27:
1497:info:build In file included from clustalW/Clustal.h:15:
1498:info:build In file included from clustalW/general/clustalw.h:42:
1499:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1500:info:build            int y = x.size();
1501:info:build                ^
1502:info:build In file included from TreeFormatOptions.cpp:7:
1503:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1504:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1505:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1506:info:build     char type;
1507:info:build          ^
1508:info:build In file included from TreeFormatOptions.cpp:11:
1509:info:build In file included from ./clustalW/general/userparams.h:8:
1510:info:build In file included from clustalW/general/UserParameters.h:22:
1511:info:build In file included from clustalW/general/utils.h:8:
1512:info:build In file included from clustalW/general/Utility.h:15:
1513:info:build In file included from clustalW/general/clustalw.h:44:
1514:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1515:info:build         int firstSeq, numSeqsInSub;
1516:info:build             ^
1517:info:build In file included from clustalW/Clustal.cpp:27:
1518:info:build In file included from clustalW/Clustal.h:15:
1519:info:build In file included from clustalW/general/clustalw.h:43:
1520:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1521:info:build            int y = x.size();
1522:info:build                ^
1523:info:build 7 warnings generated.
1524: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
1525:info:build 4 warnings generated.
1526: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
1527:info:build In file included from clustalW/Clustal.cpp:27:
1528:info:build In file included from clustalW/Clustal.h:18:
1529:info:build In file included from clustalW/fileInput/FileReader.h:12:
1530:info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42:
1531:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1532:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1533:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1534:info:build                                                              ^
1535:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1536:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1537:info:build                                                                  ^
1538:info:build In file included from TreeOutputFileNames.cpp:17:
1539:info:build In file included from ./TreeOutputFileNames.h:10:
1540:info:build In file included from ./ClustalQtParams.h:13:
1541:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1542:info:build In file included from clustalW/alignment/Sequence.h:20:
1543:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1544:info:build In file included from clustalW/general/UserParameters.h:22:
1545:info:build In file included from clustalW/general/utils.h:8:
1546:info:build In file included from clustalW/general/Utility.h:15:
1547:info:build In file included from clustalW/general/clustalw.h:42:
1548:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1549:info:build            int y = x.size();
1550:info:build                ^
1551:info:build In file included from TreeOutputFileNames.cpp:17:
1552:info:build In file included from ./TreeOutputFileNames.h:10:
1553:info:build In file included from ./ClustalQtParams.h:13:
1554:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1555:info:build In file included from clustalW/alignment/Sequence.h:20:
1556:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1557:info:build In file included from clustalW/general/UserParameters.h:22:
1558:info:build In file included from clustalW/general/utils.h:8:
1559:info:build In file included from clustalW/general/Utility.h:15:
1560:info:build In file included from clustalW/general/clustalw.h:43:
1561:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1562:info:build            int y = x.size();
1563:info:build                ^
1564:info:build In file included from WritePostscriptFile.cpp:24:
1565:info:build In file included from ./WritePostscriptFile.h:10:
1566:info:build In file included from ./ClustalQtParams.h:13:
1567:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1568:info:build In file included from clustalW/alignment/Sequence.h:20:
1569:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1570:info:build In file included from clustalW/general/UserParameters.h:22:
1571:info:build In file included from clustalW/general/utils.h:8:
1572:info:build In file included from clustalW/general/Utility.h:15:
1573:info:build In file included from clustalW/general/clustalw.h:42:
1574:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1575:info:build            int y = x.size();
1576:info:build                ^
1577:info:build In file included from WritePostscriptFile.cpp:24:
1578:info:build In file included from ./WritePostscriptFile.h:10:
1579:info:build In file included from ./ClustalQtParams.h:13:
1580:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1581:info:build In file included from clustalW/alignment/Sequence.h:20:
1582:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1583:info:build In file included from clustalW/general/UserParameters.h:22:
1584:info:build In file included from clustalW/general/utils.h:8:
1585:info:build In file included from clustalW/general/Utility.h:15:
1586:info:build In file included from clustalW/general/clustalw.h:43:
1587:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1588:info:build            int y = x.size();
1589:info:build                ^
1590:info:build In file included from TreeOutputFileNames.cpp:17:
1591:info:build In file included from ./TreeOutputFileNames.h:10:
1592:info:build In file included from ./ClustalQtParams.h:13:
1593:info:build In file included from ./clustalW/alignment/Alignment.h:42:
1594:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1595:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1596:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1597:info:build                                                              ^
1598:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1599:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1600:info:build                                                                  ^
1601:info:build In file included from clustalW/Clustal.cpp:27:
1602:info:build In file included from clustalW/Clustal.h:15:
1603:info:build In file included from clustalW/general/clustalw.h:44:
1604:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1605:info:build         int firstSeq, numSeqsInSub;
1606:info:build             ^
1607: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
1608:info:build In file included from WritePostscriptFile.cpp:24:
1609:info:build In file included from ./WritePostscriptFile.h:10:
1610:info:build In file included from ./ClustalQtParams.h:13:
1611:info:build In file included from ./clustalW/alignment/Alignment.h:42:
1612:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1613:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1614:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1615:info:build                                                              ^
1616:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1617:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1618:info:build                                                                  ^
1619:info:build In file included from TreeOutputFileNames.cpp:14:
1620:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1621:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1622:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1623:info:build     char type;
1624:info:build          ^
1625:info:build In file included from TreeOutputFileNames.cpp:17:
1626:info:build In file included from ./TreeOutputFileNames.h:10:
1627:info:build In file included from ./ClustalQtParams.h:13:
1628:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1629:info:build In file included from clustalW/alignment/Sequence.h:20:
1630:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1631:info:build In file included from clustalW/general/UserParameters.h:22:
1632:info:build In file included from clustalW/general/utils.h:8:
1633:info:build In file included from clustalW/general/Utility.h:15:
1634:info:build In file included from clustalW/general/clustalw.h:44:
1635:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1636:info:build         int firstSeq, numSeqsInSub;
1637:info:build             ^
1638:info:build In file included from clustalW/alignment/Alignment.cpp:25:
1639:info:build In file included from clustalW/alignment/Alignment.h:41:
1640:info:build In file included from clustalW/alignment/Sequence.h:20:
1641:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1642:info:build In file included from clustalW/general/UserParameters.h:22:
1643:info:build In file included from clustalW/general/utils.h:8:
1644:info:build In file included from clustalW/general/Utility.h:15:
1645:info:build In file included from clustalW/general/clustalw.h:42:
1646:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1647:info:build            int y = x.size();
1648:info:build                ^
1649:info:build In file included from clustalW/alignment/Alignment.cpp:25:
1650:info:build In file included from clustalW/alignment/Alignment.h:41:
1651:info:build In file included from clustalW/alignment/Sequence.h:20:
1652:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1653:info:build In file included from clustalW/general/UserParameters.h:22:
1654:info:build In file included from clustalW/general/utils.h:8:
1655:info:build In file included from clustalW/general/Utility.h:15:
1656:info:build In file included from clustalW/general/clustalw.h:43:
1657:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1658:info:build            int y = x.size();
1659:info:build                ^
1660:info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27:
1661:info:build In file included from clustalW/alignment/AlignmentOutput.h:24:
1662:info:build In file included from clustalW/alignment/Alignment.h:41:
1663:info:build In file included from clustalW/alignment/Sequence.h:20:
1664:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1665:info:build In file included from clustalW/general/UserParameters.h:22:
1666:info:build In file included from clustalW/general/utils.h:8:
1667:info:build In file included from clustalW/general/Utility.h:15:
1668:info:build In file included from clustalW/general/clustalw.h:42:
1669:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1670:info:build            int y = x.size();
1671:info:build                ^
1672:info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27:
1673:info:build In file included from clustalW/alignment/Alignment.cpp:25:
1674:info:build In file included from clustalW/alignment/Alignment.h:42:
1675:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1676:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1677:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");In file included from clustalW/alignment/AlignmentOutput.h:24:
1678:info:build In file included from clustalW/alignment/Alignment.h:41:
1679:info:build In file included from clustalW/alignment/Sequence.h:20:
1680:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1681:info:build In file included from clustalW/general/UserParameters.h:22:
1682:info:build In file included from clustalW/general/utils.h:8:
1683:info:build In file included from clustalW/general/Utility.h:15:
1684:info:build In file included from clustalW/general/clustalw.h:43:
1685:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1686:info:build            int y = x.size();
1687:info:build                ^
1688:info:build
1689:info:build                                                              ^
1690:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1691:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1692:info:build                                                                  ^
1693:info:build In file included from WritePostscriptFile.cpp:21:
1694:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/QtGui:62:
1695:info:build In file included from /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Headers/qevent.h:52:
1696:info:build /opt/local/include/QtGui/qmime.h:119:10: warning: private field 'type' is not used [-Wunused-private-field]
1697:info:build     char type;
1698:info:build          ^
1699:info:build In file included from WritePostscriptFile.cpp:24:
1700:info:build In file included from ./WritePostscriptFile.h:10:
1701:info:build In file included from ./ClustalQtParams.h:13:
1702:info:build In file included from ./clustalW/alignment/Alignment.h:41:
1703:info:build In file included from clustalW/alignment/Sequence.h:20:
1704:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1705:info:build In file included from clustalW/general/UserParameters.h:22:
1706:info:build In file included from clustalW/general/utils.h:8:
1707:info:build In file included from clustalW/general/Utility.h:15:
1708:info:build In file included from clustalW/general/clustalw.h:44:
1709:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1710:info:build         int firstSeq, numSeqsInSub;
1711:info:build             ^
1712:info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27:
1713:info:build In file included from clustalW/alignment/AlignmentOutput.h:24:
1714:info:build In file included from clustalW/alignment/Alignment.h:42:
1715:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1716:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1717:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1718:info:build                                                              ^
1719:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1720:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1721:info:build                                                                  ^
1722:info:build clustalW/alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable]
1723:info:build     SeqArray::iterator posToAddTo = sectionToRealign.begin();
1724:info:build                        ^
1725:info:build 6 warnings generated.
1726: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
1727:info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10:
1728:info:build In file included from clustalW/alignment/ObjectiveScore.h:14:
1729:info:build In file included from clustalW/alignment/../general/clustalw.h:42:
1730:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1731:info:build            int y = x.size();
1732:info:build                ^
1733:info:build In file included from clustalW/alignment/Sequence.cpp:10:
1734:info:build In file included from clustalW/alignment/Sequence.h:20:
1735:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1736:info:build In file included from clustalW/general/UserParameters.h:22:
1737:info:build In file included from clustalW/general/utils.h:8:
1738:info:build In file included from clustalW/general/Utility.h:15:
1739:info:build In file included from clustalW/general/clustalw.h:42:
1740:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1741:info:build            int y = x.size();
1742:info:build                ^
1743:info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10:
1744:info:build In file included from clustalW/alignment/ObjectiveScore.h:14:
1745:info:build In file included from clustalW/alignment/../general/clustalw.h:43:
1746:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1747:info:build            int y = x.size();
1748:info:build                ^
1749:info:build In file included from clustalW/alignment/Sequence.cpp:10:
1750:info:build In file included from clustalW/alignment/Sequence.h:20:
1751:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1752:info:build In file included from clustalW/general/UserParameters.h:22:
1753:info:build In file included from clustalW/general/utils.h:8:
1754:info:build In file included from clustalW/general/Utility.h:15:
1755:info:build In file included from clustalW/general/clustalw.h:43:
1756:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1757:info:build            int y = x.size();
1758:info:build                ^
1759:info:build In file included from clustalW/alignment/Alignment.cpp:25:
1760:info:build In file included from clustalW/alignment/Alignment.h:41:
1761:info:build In file included from clustalW/alignment/Sequence.h:20:
1762:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1763:info:build In file included from clustalW/general/UserParameters.h:22:
1764:info:build In file included from clustalW/general/utils.h:8:
1765:info:build In file included from clustalW/general/Utility.h:15:
1766:info:build In file included from clustalW/general/clustalw.h:44:
1767:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1768:info:build         int firstSeq, numSeqsInSub;
1769:info:build             ^
1770:info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10:
1771:info:build In file included from clustalW/alignment/ObjectiveScore.h:15:
1772:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1773:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1774:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1775:info:build                                                              ^
1776:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1777:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1778:info:build                                                                  ^
1779:info:build In file included from clustalW/alignment/Sequence.cpp:10:
1780:info:build In file included from clustalW/alignment/Sequence.h:20:
1781:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1782:info:build In file included from clustalW/general/UserParameters.h:22:
1783:info:build In file included from clustalW/general/utils.h:8:
1784:info:build In file included from clustalW/general/Utility.h:15:
1785:info:build In file included from clustalW/general/clustalw.h:44:
1786:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1787:info:build         int firstSeq, numSeqsInSub;
1788:info:build             ^
1789:info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10:
1790:info:build In file included from clustalW/alignment/ObjectiveScore.h:14:
1791:info:build In file included from clustalW/alignment/../general/clustalw.h:44:
1792:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1793:info:build         int firstSeq, numSeqsInSub;
1794:info:build             ^
1795:info:build In file included from clustalW/alignment/ObjectiveScore.cpp:10:
1796:info:build clustalW/alignment/ObjectiveScore.h:40:14: warning: private field 'scale' is not used [-Wunused-private-field]
1797:info:build         long scale;
1798:info:build              ^
1799:info:build clustalW/alignment/ObjectiveScore.h:41:13: warning: private field 'weightScale' is not used [-Wunused-private-field]
1800:info:build         int weightScale;
1801:info:build             ^
1802:info:build clustalW/alignment/ObjectiveScore.h:42:13: warning: private field 'sagaGapEx' is not used [-Wunused-private-field]
1803:info:build         int sagaGapEx, sagaGapOp;
1804:info:build             ^
1805:info:build clustalW/alignment/ObjectiveScore.h:42:24: warning: private field 'sagaGapOp' is not used [-Wunused-private-field]
1806:info:build         int sagaGapEx, sagaGapOp;
1807:info:build                        ^
1808:info:build In file included from clustalW/alignment/AlignmentOutput.cpp:27:
1809:info:build In file included from clustalW/alignment/AlignmentOutput.h:24:
1810:info:build In file included from clustalW/alignment/Alignment.h:41:
1811:info:build In file included from clustalW/alignment/Sequence.h:20:
1812:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1813:info:build In file included from clustalW/general/UserParameters.h:22:
1814:info:build In file included from clustalW/general/utils.h:8:
1815:info:build In file included from clustalW/general/Utility.h:15:
1816:info:build In file included from clustalW/general/clustalw.h:44:
1817:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1818:info:build         int firstSeq, numSeqsInSub;
1819:info:build             ^
1820:info:build 6 warnings generated.
1821: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
1822:info:build In file included from clustalW/fileInput/ClustalFileParser.cpp:19:
1823:info:build In file included from clustalW/fileInput/ClustalFileParser.h:10:
1824:info:build In file included from clustalW/fileInput/FileParser.h:22:
1825:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1826:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1827:info:build In file included from clustalW/general/UserParameters.h:22:
1828:info:build In file included from clustalW/general/utils.h:8:
1829:info:build In file included from clustalW/general/Utility.h:15:
1830:info:build In file included from clustalW/general/clustalw.h:42:
1831:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1832:info:build            int y = x.size();
1833:info:build                ^
1834:info:build 9 warnings generated.
1835:info:build In file included from clustalW/fileInput/ClustalFileParser.cpp:19:
1836:info:build In file included from clustalW/fileInput/ClustalFileParser.h:10:
1837:info:build In file included from clustalW/fileInput/FileParser.h:22:
1838:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1839:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1840:info:build In file included from clustalW/general/UserParameters.h:22:
1841:info:build In file included from clustalW/general/utils.h:8:
1842:info:build In file included from clustalW/general/Utility.h:15:
1843:info:build In file included from clustalW/general/clustalw.h:43:
1844:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1845:info:build            int y = x.size();
1846:info:build                ^
1847: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
1848:info:build 3 warnings generated.
1849: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
1850:info:build In file included from clustalW/fileInput/ClustalFileParser.cpp:19:
1851:info:build In file included from clustalW/fileInput/ClustalFileParser.h:10:
1852:info:build In file included from clustalW/fileInput/FileParser.h:22:
1853:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1854:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1855:info:build In file included from clustalW/general/UserParameters.h:22:
1856:info:build In file included from clustalW/general/utils.h:8:
1857:info:build In file included from clustalW/general/Utility.h:15:
1858:info:build In file included from clustalW/general/clustalw.h:44:
1859:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1860:info:build         int firstSeq, numSeqsInSub;
1861:info:build             ^
1862:info:build In file included from clustalW/fileInput/EMBLFileParser.cpp:16:
1863:info:build In file included from clustalW/fileInput/EMBLFileParser.h:10:
1864:info:build In file included from clustalW/fileInput/FileParser.h:22:
1865:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1866:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1867:info:build In file included from clustalW/general/UserParameters.h:22:
1868:info:build In file included from clustalW/general/utils.h:8:
1869:info:build In file included from clustalW/general/Utility.h:15:
1870:info:build In file included from clustalW/general/clustalw.h:42:
1871:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1872:info:build            int y = x.size();
1873:info:build                ^
1874:info:build In file included from clustalW/fileInput/EMBLFileParser.cpp:16:
1875:info:build In file included from clustalW/fileInput/EMBLFileParser.h:10:
1876:info:build In file included from clustalW/fileInput/FileParser.h:22:
1877:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1878:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1879:info:build In file included from clustalW/general/UserParameters.h:22:
1880:info:build In file included from clustalW/general/utils.h:8:
1881:info:build In file included from clustalW/general/Utility.h:15:
1882:info:build In file included from clustalW/general/clustalw.h:43:
1883:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1884:info:build            int y = x.size();
1885:info:build                ^
1886:info:build 3 warnings generated.
1887: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
1888:info:build In file included from clustalW/fileInput/EMBLFileParser.cpp:16:
1889:info:build In file included from clustalW/fileInput/EMBLFileParser.h:10:
1890:info:build In file included from clustalW/fileInput/FileParser.h:22:
1891:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1892:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1893:info:build In file included from clustalW/general/UserParameters.h:22:
1894:info:build In file included from clustalW/general/utils.h:8:
1895:info:build In file included from clustalW/general/Utility.h:15:
1896:info:build In file included from clustalW/general/clustalw.h:44:
1897:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1898:info:build         int firstSeq, numSeqsInSub;
1899:info:build             ^
1900:info:build 5 warnings generated.
1901: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
1902:info:build In file included from clustalW/fileInput/FileParser.cpp:14:
1903:info:build In file included from clustalW/fileInput/FileParser.h:22:
1904:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1905:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1906:info:build In file included from clustalW/general/UserParameters.h:22:
1907:info:build In file included from clustalW/general/utils.h:8:
1908:info:build In file included from clustalW/general/Utility.h:15:
1909:info:build In file included from clustalW/general/clustalw.h:42:
1910:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1911:info:build            int y = x.size();
1912:info:build                ^
1913:info:build In file included from clustalW/fileInput/FileParser.cpp:14:
1914:info:build In file included from clustalW/fileInput/FileParser.h:22:
1915:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1916:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1917:info:build In file included from clustalW/general/UserParameters.h:22:
1918:info:build In file included from clustalW/general/utils.h:8:
1919:info:build In file included from clustalW/general/Utility.h:15:
1920:info:build In file included from clustalW/general/clustalw.h:43:
1921:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1922:info:build            int y = x.size();
1923:info:build                ^
1924:info:build In file included from clustalW/fileInput/FileReader.cpp:29:
1925:info:build In file included from clustalW/fileInput/FileReader.h:12:
1926:info:build In file included from clustalW/fileInput/../alignment/Alignment.h:41:
1927:info:build In file included from clustalW/alignment/Sequence.h:20:
1928:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1929:info:build In file included from clustalW/general/UserParameters.h:22:
1930:info:build In file included from clustalW/general/utils.h:8:
1931:info:build In file included from clustalW/general/Utility.h:15:
1932:info:build In file included from clustalW/general/clustalw.h:42:
1933:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1934:info:build            int y = x.size();
1935:info:build                ^
1936:info:build In file included from clustalW/fileInput/FileReader.cpp:29:
1937:info:build In file included from clustalW/fileInput/FileReader.h:12:
1938:info:build In file included from clustalW/fileInput/../alignment/Alignment.h:41:
1939:info:build In file included from clustalW/alignment/Sequence.h:20:
1940:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1941:info:build In file included from clustalW/general/UserParameters.h:22:
1942:info:build In file included from clustalW/general/utils.h:8:
1943:info:build In file included from clustalW/general/Utility.h:15:
1944:info:build In file included from clustalW/general/clustalw.h:43:
1945:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1946:info:build            int y = x.size();
1947:info:build                ^
1948:info:build In file included from clustalW/fileInput/GDEFileParser.cpp:16:
1949:info:build In file included from clustalW/fileInput/GDEFileParser.h:10:
1950:info:build In file included from clustalW/fileInput/FileParser.h:22:
1951:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1952:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1953:info:build In file included from clustalW/general/UserParameters.h:22:
1954:info:build In file included from clustalW/general/utils.h:8:
1955:info:build In file included from clustalW/general/Utility.h:15:
1956:info:build In file included from clustalW/general/clustalw.h:42:
1957:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
1958:info:build            int y = x.size();
1959:info:build                ^
1960:info:build In file included from clustalW/fileInput/GDEFileParser.cpp:16:
1961:info:build In file included from clustalW/fileInput/GDEFileParser.h:10:
1962:info:build In file included from clustalW/fileInput/FileParser.h:22:
1963:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1964:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1965:info:build In file included from clustalW/general/UserParameters.h:22:
1966:info:build In file included from clustalW/general/utils.h:8:
1967:info:build In file included from clustalW/general/Utility.h:15:
1968:info:build In file included from clustalW/general/clustalw.h:43:
1969:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
1970:info:build            int y = x.size();
1971:info:build                ^
1972:info:build In file included from clustalW/fileInput/FileParser.cpp:14:
1973:info:build In file included from clustalW/fileInput/FileParser.h:22:
1974:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1975:info:build In file included from clustalW/alignment/../general/userparams.h:8:
1976:info:build In file included from clustalW/general/UserParameters.h:22:
1977:info:build In file included from clustalW/general/utils.h:8:
1978:info:build In file included from clustalW/general/Utility.h:15:
1979:info:build In file included from clustalW/general/clustalw.h:44:
1980:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
1981:info:build         int firstSeq, numSeqsInSub;
1982:info:build             ^
1983:info:build In file included from clustalW/fileInput/FileReader.cpp:29:
1984:info:build In file included from clustalW/fileInput/FileReader.h:12:
1985:info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42:
1986:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
1987:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1988:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
1989:info:build                                                              ^
1990:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
1991:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
1992:info:build                                                                  ^
1993:info:build 3 warnings generated.
1994: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
1995:info:build In file included from clustalW/fileInput/GDEFileParser.cpp:16:
1996:info:build In file included from clustalW/fileInput/GDEFileParser.h:10:
1997:info:build In file included from clustalW/fileInput/FileParser.h:22:
1998:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
1999:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2000:info:build In file included from clustalW/general/UserParameters.h:22:
2001:info:build In file included from clustalW/general/utils.h:8:
2002:info:build In file included from clustalW/general/Utility.h:15:
2003:info:build In file included from clustalW/general/clustalw.h:44:
2004:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2005:info:build         int firstSeq, numSeqsInSub;
2006:info:build             ^
2007:info:build 3 warnings generated.
2008: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
2009:info:build In file included from clustalW/fileInput/FileReader.cpp:29:
2010:info:build In file included from clustalW/fileInput/FileReader.h:12:
2011:info:build In file included from clustalW/fileInput/../alignment/Alignment.h:41:
2012:info:build In file included from clustalW/alignment/Sequence.h:20:
2013:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2014:info:build In file included from clustalW/general/UserParameters.h:22:
2015:info:build In file included from clustalW/general/utils.h:8:
2016:info:build In file included from clustalW/general/Utility.h:15:
2017:info:build In file included from clustalW/general/clustalw.h:44:
2018:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2019:info:build         int firstSeq, numSeqsInSub;
2020:info:build             ^
2021:info:build 3 warnings generated.
2022: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
2023:info:build In file included from clustalW/fileInput/MSFFileParser.cpp:16:
2024:info:build In file included from clustalW/fileInput/MSFFileParser.h:10:
2025:info:build In file included from clustalW/fileInput/FileParser.h:22:
2026:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2027:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2028:info:build In file included from clustalW/general/UserParameters.h:22:
2029:info:build In file included from clustalW/general/utils.h:8:
2030:info:build In file included from clustalW/general/Utility.h:15:
2031:info:build In file included from clustalW/general/clustalw.h:42:
2032:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2033:info:build            int y = x.size();
2034:info:build                ^
2035:info:build In file included from clustalW/fileInput/MSFFileParser.cpp:16:
2036:info:build In file included from clustalW/fileInput/MSFFileParser.h:10:
2037:info:build In file included from clustalW/fileInput/FileParser.h:22:
2038:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2039:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2040:info:build In file included from clustalW/general/UserParameters.h:22:
2041:info:build In file included from clustalW/general/utils.h:8:
2042:info:build In file included from clustalW/general/Utility.h:15:
2043:info:build In file included from clustalW/general/clustalw.h:43:
2044:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2045:info:build            int y = x.size();
2046:info:build                ^
2047: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
2048:info:build clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
2049:info:build     vector<Sequence> MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq)
2050:info:build                                                                               ^
2051:info:build clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
2052:info:build void MSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
2053:info:build                                                   ^
2054:info:build clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter]
2055:info:build void MSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
2056:info:build                                                                                 ^
2057:info:build clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter]
2058:info:build                                     string& secStructName, int &structPenalties, int length)
2059:info:build                                             ^
2060:info:build clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter]
2061:info:build                                     string& secStructName, int &structPenalties, int length)
2062:info:build                                                                                      ^
2063:info:build 5 warnings generated.
2064: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
2065:info:build In file included from clustalW/fileInput/MSFFileParser.cpp:16:
2066:info:build In file included from clustalW/fileInput/MSFFileParser.h:10:
2067:info:build In file included from clustalW/fileInput/FileParser.h:22:
2068:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2069:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2070:info:build In file included from clustalW/general/UserParameters.h:22:
2071:info:build In file included from clustalW/general/utils.h:8:
2072:info:build In file included from clustalW/general/Utility.h:15:
2073:info:build In file included from clustalW/general/clustalw.h:44:
2074:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2075:info:build         int firstSeq, numSeqsInSub;
2076:info:build             ^
2077:info:build In file included from clustalW/fileInput/PearsonFileParser.cpp:26:
2078:info:build In file included from clustalW/fileInput/PearsonFileParser.h:14:
2079:info:build In file included from clustalW/fileInput/FileParser.h:22:
2080:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2081:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2082:info:build In file included from clustalW/general/UserParameters.h:22:
2083:info:build In file included from clustalW/general/utils.h:8:
2084:info:build In file included from clustalW/general/Utility.h:15:
2085:info:build In file included from clustalW/general/clustalw.h:42:
2086:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2087:info:build            int y = x.size();
2088:info:build                ^
2089:info:build In file included from clustalW/fileInput/PearsonFileParser.cpp:26:
2090:info:build In file included from clustalW/fileInput/PearsonFileParser.h:14:
2091:info:build In file included from clustalW/fileInput/FileParser.h:22:
2092:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2093:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2094:info:build In file included from clustalW/general/UserParameters.h:22:
2095:info:build In file included from clustalW/general/utils.h:8:
2096:info:build In file included from clustalW/general/Utility.h:15:
2097:info:build In file included from clustalW/general/clustalw.h:43:
2098:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2099:info:build            int y = x.size();
2100:info:build                ^
2101:info:build 5 warnings generated.
2102: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
2103:info:build 6 warnings generated.
2104: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
2105:info:build In file included from clustalW/fileInput/PIRFileParser.cpp:16:
2106:info:build In file included from clustalW/fileInput/PIRFileParser.h:10:
2107:info:build In file included from clustalW/fileInput/FileParser.h:22:
2108:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2109:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2110:info:build In file included from clustalW/general/UserParameters.h:22:
2111:info:build In file included from clustalW/general/utils.h:8:
2112:info:build In file included from clustalW/general/Utility.h:15:
2113:info:build In file included from clustalW/general/clustalw.h:42:
2114:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2115:info:build            int y = x.size();
2116:info:build                ^
2117:info:build In file included from clustalW/fileInput/PIRFileParser.cpp:16:
2118:info:build In file included from clustalW/fileInput/PIRFileParser.h:10:
2119:info:build In file included from clustalW/fileInput/FileParser.h:22:
2120:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2121:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2122:info:build In file included from clustalW/general/UserParameters.h:22:
2123:info:build In file included from clustalW/general/utils.h:8:
2124:info:build In file included from clustalW/general/Utility.h:15:
2125:info:build In file included from clustalW/general/clustalw.h:43:
2126:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2127:info:build            int y = x.size();
2128:info:build                ^
2129:info:build clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
2130:info:build     Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq)
2131:info:build                                                            ^
2132:info:build clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
2133:info:build void PearsonFileParser::getSecStructure(vector<char>& gapPenaltyMask,
2134:info:build                                                       ^
2135:info:build clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter]
2136:info:build                          vector<char>& secStructMask, string& secStructName,
2137:info:build                                        ^
2138:info:build clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter]
2139:info:build                          vector<char>& secStructMask, string& secStructName,
2140:info:build                                                               ^
2141:info:build clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter]
2142:info:build                           int &structPenalties, int length)
2143:info:build                                                     ^
2144:info:build In file included from clustalW/fileInput/PearsonFileParser.cpp:26:
2145:info:build In file included from clustalW/fileInput/PearsonFileParser.h:14:
2146:info:build In file included from clustalW/fileInput/FileParser.h:22:
2147:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2148:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2149:info:build In file included from clustalW/general/UserParameters.h:22:
2150:info:build In file included from clustalW/general/utils.h:8:
2151:info:build In file included from clustalW/general/Utility.h:15:
2152:info:build In file included from clustalW/general/clustalw.h:44:
2153:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2154:info:build         int firstSeq, numSeqsInSub;
2155:info:build             ^
2156:info:build 8 warnings generated.
2157: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
2158:info:build clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
2159:info:build void PIRFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
2160:info:build                                                   ^
2161:info:build clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter 'secStructMask' [-Wunused-parameter]
2162:info:build void PIRFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
2163:info:build                                                                                 ^
2164:info:build clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter 'secStructName' [-Wunused-parameter]
2165:info:build                                     string& secStructName, int &structPenalties, int length)
2166:info:build                                             ^
2167:info:build clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter]
2168:info:build                                     string& secStructName, int &structPenalties, int length)
2169:info:build                                                                                      ^
2170:info:build In file included from clustalW/fileInput/PIRFileParser.cpp:16:
2171:info:build In file included from clustalW/fileInput/PIRFileParser.h:10:
2172:info:build In file included from clustalW/fileInput/FileParser.h:22:
2173:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2174:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2175:info:build In file included from clustalW/general/UserParameters.h:22:
2176:info:build In file included from clustalW/general/utils.h:8:
2177:info:build In file included from clustalW/general/Utility.h:15:
2178:info:build In file included from clustalW/general/clustalw.h:44:
2179:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2180:info:build         int firstSeq, numSeqsInSub;
2181:info:build             ^
2182:info:build In file included from clustalW/fileInput/RSFFileParser.cpp:16:
2183:info:build In file included from clustalW/fileInput/RSFFileParser.h:10:
2184:info:build In file included from clustalW/fileInput/FileParser.h:22:
2185:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2186:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2187:info:build In file included from clustalW/general/UserParameters.h:22:
2188:info:build In file included from clustalW/general/utils.h:8:
2189:info:build In file included from clustalW/general/Utility.h:15:
2190:info:build In file included from clustalW/general/clustalw.h:42:
2191:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2192:info:build            int y = x.size();
2193:info:build                ^
2194:info:build In file included from clustalW/fileInput/RSFFileParser.cpp:16:
2195:info:build In file included from clustalW/fileInput/RSFFileParser.h:10:
2196:info:build In file included from clustalW/fileInput/FileParser.h:22:
2197:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2198:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2199:info:build In file included from clustalW/general/UserParameters.h:22:
2200:info:build In file included from clustalW/general/utils.h:8:
2201:info:build In file included from clustalW/general/Utility.h:15:
2202:info:build In file included from clustalW/general/clustalw.h:43:
2203:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2204:info:build            int y = x.size();
2205:info:build                ^
2206:info:build In file included from clustalW/general/ClustalWResources.cpp:14:
2207:info:build In file included from clustalW/general/clustalw.h:42:
2208:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2209:info:build            int y = x.size();
2210:info:build                ^
2211:info:build 7 warnings generated.
2212:info:build In file included from clustalW/general/ClustalWResources.cpp:14:
2213:info:build In file included from clustalW/general/clustalw.h:43:
2214:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2215:info:build            int y = x.size();
2216:info:build                ^
2217:info:build clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
2218:info:build void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
2219:info:build                                                   ^
2220: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
2221:info:build In file included from clustalW/fileInput/RSFFileParser.cpp:16:
2222:info:build In file included from clustalW/fileInput/RSFFileParser.h:10:
2223:info:build In file included from clustalW/fileInput/FileParser.h:22:
2224:info:build In file included from clustalW/fileInput/../alignment/Sequence.h:20:
2225:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2226:info:build In file included from clustalW/general/UserParameters.h:22:
2227:info:build In file included from clustalW/general/utils.h:8:
2228:info:build In file included from clustalW/general/Utility.h:15:
2229:info:build In file included from clustalW/general/clustalw.h:44:
2230:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2231:info:build         int firstSeq, numSeqsInSub;
2232:info:build             ^
2233: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]
2234:info:build     delim[1] = 0;
2235:info:build     ^     ~
2236:info:build clustalW/general/ClustalWResources.cpp:104:5: note: array 'delim' declared here
2237:info:build     char delim[1];
2238:info:build     ^
2239:info:build In file included from clustalW/general/ClustalWResources.cpp:14:
2240:info:build In file included from clustalW/general/clustalw.h:44:
2241:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2242:info:build         int firstSeq, numSeqsInSub;
2243:info:build             ^
2244:info:build 8 warnings generated.
2245: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
2246:info:build In file included from clustalW/general/OutputFile.cpp:10:
2247:info:build In file included from clustalW/general/utils.h:8:
2248:info:build In file included from clustalW/general/Utility.h:15:
2249:info:build In file included from clustalW/general/clustalw.h:42:
2250:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2251:info:build            int y = x.size();
2252:info:build                ^
2253:info:build In file included from clustalW/general/OutputFile.cpp:10:
2254:info:build In file included from clustalW/general/utils.h:8:
2255:info:build In file included from clustalW/general/Utility.h:15:
2256:info:build In file included from clustalW/general/clustalw.h:43:
2257:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2258:info:build            int y = x.size();
2259:info:build                ^
2260:info:build In file included from clustalW/general/Stats.cpp:15:
2261:info:build In file included from clustalW/general/../alignment/Alignment.h:41:
2262:info:build In file included from clustalW/alignment/Sequence.h:20:
2263:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2264:info:build In file included from clustalW/general/UserParameters.h:22:
2265:info:build In file included from clustalW/general/utils.h:8:
2266:info:build In file included from clustalW/general/Utility.h:15:
2267:info:build In file included from clustalW/general/clustalw.h:42:
2268:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2269:info:build            int y = x.size();
2270:info:build                ^
2271:info:build In file included from clustalW/general/Stats.cpp:15:
2272:info:build In file included from clustalW/general/../alignment/Alignment.h:41:
2273:info:build In file included from clustalW/alignment/Sequence.h:20:
2274:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2275:info:build In file included from clustalW/general/UserParameters.h:22:
2276:info:build In file included from clustalW/general/utils.h:8:
2277:info:build In file included from clustalW/general/Utility.h:15:
2278:info:build In file included from clustalW/general/clustalw.h:43:
2279:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2280:info:build            int y = x.size();
2281:info:build                ^
2282:info:build In file included from clustalW/general/OutputFile.cpp:10:
2283:info:build In file included from clustalW/general/utils.h:8:
2284:info:build In file included from clustalW/general/Utility.h:15:
2285:info:build In file included from clustalW/general/clustalw.h:44:
2286:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2287:info:build         int firstSeq, numSeqsInSub;
2288:info:build             ^
2289:info:build In file included from clustalW/general/Stats.cpp:15:
2290:info:build In file included from clustalW/general/../alignment/Alignment.h:42:
2291:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
2292:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2293:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
2294:info:build                                                              ^
2295:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2296:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
2297:info:build                                                                  ^
2298:info:build 4 warnings generated.
2299: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
2300:info:build In file included from clustalW/general/Stats.cpp:15:
2301:info:build In file included from clustalW/general/../alignment/Alignment.h:41:
2302:info:build In file included from clustalW/alignment/Sequence.h:20:
2303:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2304:info:build In file included from clustalW/general/UserParameters.h:22:
2305:info:build In file included from clustalW/general/utils.h:8:
2306:info:build In file included from clustalW/general/Utility.h:15:
2307:info:build In file included from clustalW/general/clustalw.h:44:
2308:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2309:info:build         int firstSeq, numSeqsInSub;
2310:info:build             ^
2311: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
2312:info:build 4 warnings generated.
2313: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
2314:info:build In file included from clustalW/general/SymMatrix.cpp:10:
2315:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2316:info:build         int firstSeq, numSeqsInSub;
2317:info:build             ^
2318:info:build 1 warning generated.
2319: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
2320:info:build In file included from clustalW/general/VectorOutOfRange.cpp:9:
2321:info:build clustalW/general/VectorOutOfRange.h:23:21: error: implicit instantiation of undefined template 'std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >'
2322:info:build         std::string _name;
2323:info:build                     ^
2324:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:188:33: note: template is declared here
2325:info:build     class _LIBCPP_TYPE_VIS_ONLY basic_string;
2326:info:build                                 ^
2327:info:build In file included from clustalW/general/VectorOutOfRange.cpp:9:
2328:info:build clustalW/general/VectorOutOfRange.h:14:38: error: implicit instantiation of undefined template 'std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >'
2329:info:build         VectorOutOfRange(std::string vectorName, int index, int max)
2330:info:build                                      ^
2331:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:188:33: note: template is declared here
2332:info:build     class _LIBCPP_TYPE_VIS_ONLY basic_string;
2333:info:build                                 ^
2334:info:build In file included from clustalW/general/VectorOutOfRange.cpp:9:
2335:info:build clustalW/general/VectorOutOfRange.h:14:38: warning: unused parameter 'vectorName' [-Wunused-parameter]
2336:info:build         VectorOutOfRange(std::string vectorName, int index, int max)
2337:info:build                                      ^
2338:info:build 3 warnings generated.
2339: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
2340:info:build 5 warnings generated.
2341: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
2342:info:build In file included from clustalW/general/UserParameters.cpp:24:
2343:info:build In file included from clustalW/general/UserParameters.h:22:
2344:info:build In file included from clustalW/general/utils.h:8:
2345:info:build In file included from clustalW/general/Utility.h:15:
2346:info:build In file included from clustalW/general/clustalw.h:42:
2347:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2348:info:build            int y = x.size();
2349:info:build                ^
2350:info:build In file included from clustalW/general/UserParameters.cpp:24:
2351:info:build In file included from clustalW/general/UserParameters.h:22:
2352:info:build In file included from clustalW/general/utils.h:8:
2353:info:build In file included from clustalW/general/Utility.h:15:
2354:info:build In file included from clustalW/general/clustalw.h:43:
2355:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2356:info:build            int y = x.size();
2357:info:build                ^
2358:info:build clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter]
2359:info:build UserParameters::UserParameters(bool log)
2360:info:build                                     ^
2361:info:build In file included from clustalW/general/UserParameters.cpp:24:
2362:info:build In file included from clustalW/general/UserParameters.h:22:
2363:info:build In file included from clustalW/general/utils.h:8:
2364:info:build In file included from clustalW/general/Utility.h:15:
2365:info:build In file included from clustalW/general/clustalw.h:44:
2366:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2367:info:build         int firstSeq, numSeqsInSub;
2368:info:build             ^
2369:info:build In file included from clustalW/general/Utility.cpp:19:
2370:info:build In file included from clustalW/general/Utility.h:15:
2371:info:build In file included from clustalW/general/clustalw.h:42:
2372:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2373:info:build            int y = x.size();
2374:info:build                ^
2375:info:build In file included from clustalW/general/Utility.cpp:19:
2376:info:build In file included from clustalW/general/Utility.h:15:
2377:info:build In file included from clustalW/general/clustalw.h:43:
2378:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2379:info:build            int y = x.size();
2380:info:build                ^
2381:info:build clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter]
2382:info:build void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj)
2383:info:build                                       ^
2384:info:build In file included from clustalW/general/Utility.cpp:19:
2385:info:build In file included from clustalW/general/Utility.h:15:
2386:info:build In file included from clustalW/general/clustalw.h:44:
2387:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2388:info:build         int firstSeq, numSeqsInSub;
2389:info:build             ^
2390:info:build 1 warning and 2 errors generated.
2391:info:build make: *** [VectorOutOfRange.o] Error 1
2392:info:build make: *** Waiting for unfinished jobs....
2393:info:build In file included from clustalW/interface/InteractiveMenu.cpp:23:
2394:info:build In file included from clustalW/interface/InteractiveMenu.h:15:
2395:info:build In file included from clustalW/interface/../Clustal.h:15:
2396:info:build In file included from clustalW/general/clustalw.h:42:
2397:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2398:info:build            int y = x.size();
2399:info:build                ^
2400:info:build In file included from clustalW/interface/InteractiveMenu.cpp:23:
2401:info:build In file included from clustalW/interface/InteractiveMenu.h:15:
2402:info:build In file included from clustalW/interface/../Clustal.h:15:
2403:info:build In file included from clustalW/general/clustalw.h:43:
2404:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2405:info:build            int y = x.size();
2406:info:build                ^
2407:info:build In file included from clustalW/interface/CommandLineParser.cpp:13:
2408:info:build In file included from clustalW/interface/CommandLineParser.h:18:
2409:info:build In file included from clustalW/interface/../Clustal.h:15:
2410:info:build In file included from clustalW/general/clustalw.h:42:
2411:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2412:info:build            int y = x.size();
2413:info:build                ^
2414:info:build In file included from clustalW/multipleAlign/Iteration.cpp:13:
2415:info:build In file included from clustalW/multipleAlign/Iteration.h:8:
2416:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2417:info:build In file included from clustalW/alignment/Sequence.h:20:
2418:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2419:info:build In file included from clustalW/general/UserParameters.h:22:
2420:info:build In file included from clustalW/general/utils.h:8:
2421:info:build In file included from clustalW/general/Utility.h:15:
2422:info:build In file included from clustalW/general/clustalw.h:42:
2423:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2424:info:build            int y = x.size();
2425:info:build                ^
2426:info:build In file included from clustalW/multipleAlign/Iteration.cpp:13:
2427:info:build In file included from clustalW/multipleAlign/Iteration.h:8:
2428:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2429:info:build In file included from clustalW/alignment/Sequence.h:20:
2430:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2431:info:build In file included from clustalW/general/UserParameters.h:22:
2432:info:build In file included from clustalW/general/utils.h:8:
2433:info:build In file included from clustalW/general/Utility.h:15:
2434:info:build In file included from clustalW/general/clustalw.h:43:
2435:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2436:info:build            int y = x.size();
2437:info:build                ^
2438:info:build In file included from clustalW/interface/CommandLineParser.cpp:13:
2439:info:build In file included from clustalW/interface/CommandLineParser.h:18:
2440:info:build In file included from clustalW/interface/../Clustal.h:15:
2441:info:build In file included from clustalW/general/clustalw.h:43:
2442:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2443:info:build            int y = x.size();
2444:info:build                ^
2445:info:build In file included from clustalW/interface/InteractiveMenu.cpp:23:
2446:info:build In file included from clustalW/interface/InteractiveMenu.h:15:
2447:info:build In file included from clustalW/interface/../Clustal.h:18:
2448:info:build In file included from clustalW/fileInput/FileReader.h:12:
2449:info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42:
2450:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
2451:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2452:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
2453:info:build                                                              ^
2454:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2455:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
2456:info:build                                                                  ^
2457:info:build In file included from clustalW/multipleAlign/Iteration.cpp:13:
2458:info:build In file included from clustalW/multipleAlign/Iteration.h:84 warnings generated.
2459:info:build :
2460:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:42:
2461:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
2462:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2463:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
2464:info:build                                                              ^
2465:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2466:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
2467:info:build                                                                  ^
2468:info:build In file included from clustalW/interface/CommandLineParser.cpp:13:
2469:info:build In file included from clustalW/interface/CommandLineParser.h:18:
2470:info:build In file included from clustalW/interface/../Clustal.h:18:
2471:info:build In file included from clustalW/fileInput/FileReader.h:12:
2472:info:build In file included from clustalW/fileInput/../alignment/Alignment.h:42:
2473:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
2474:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2475:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
2476:info:build                                                              ^
2477:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2478:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
2479:info:build                                                                  ^
2480:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9:
2481:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13:
2482:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2483:info:build In file included from clustalW/alignment/Sequence.h:20:
2484:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2485:info:build In file included from clustalW/general/UserParameters.h:22:
2486:info:build In file included from clustalW/general/utils.h:8:
2487:info:build In file included from clustalW/general/Utility.h:15:
2488:info:build In file included from clustalW/general/clustalw.h:42:
2489:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2490:info:build            int y = x.size();
2491:info:build                ^
2492:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9:
2493:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13:
2494:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2495:info:build In file included from clustalW/alignment/Sequence.h:20:
2496:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2497:info:build In file included from clustalW/general/UserParameters.h:22:
2498:info:build In file included from clustalW/general/utils.h:8:
2499:info:build In file included from clustalW/general/Utility.h:15:
2500:info:build In file included from clustalW/general/clustalw.h:43:
2501:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2502:info:build            int y = x.size();
2503:info:build                ^
2504: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]
2505:info:build                 tmpnam (buffer);
2506:info:build                 ^
2507:info:build /usr/include/stdio.h:274:7: note: 'tmpnam' declared here
2508:info:build char    *tmpnam(char *);
2509:info:build          ^
2510:info:build In file included from clustalW/multipleAlign/MSA.cpp:16:
2511:info:build In file included from clustalW/multipleAlign/MSA.h:10:
2512:info:build In file included from clustalW/multipleAlign/ProfileBase.h:14:
2513:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2514:info:build In file included from clustalW/alignment/Sequence.h:20:
2515:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2516:info:build In file included from clustalW/general/UserParameters.h:22:
2517:info:build In file included from clustalW/general/utils.h:8:
2518:info:build In file included from clustalW/general/Utility.h:15:
2519:info:build In file included from clustalW/general/clustalw.h:42:
2520:info:build clustalW/general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
2521:info:build            int y = x.size();
2522:info:build                ^
2523:info:build In file included from clustalW/multipleAlign/MSA.cpp:16:
2524:info:build In file included from clustalW/multipleAlign/MSA.h:10:
2525:info:build In file included from clustalW/multipleAlign/ProfileBase.h:14:
2526:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2527:info:build In file included from clustalW/alignment/Sequence.h:20:
2528:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2529:info:build In file included from clustalW/general/UserParameters.h:22:
2530:info:build In file included from clustalW/general/utils.h:8:
2531:info:build In file included from clustalW/general/Utility.h:15:
2532:info:build In file included from clustalW/general/clustalw.h:43:
2533:info:build clustalW/general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
2534:info:build            int y = x.size();
2535:info:build                ^
2536:info:build 4 warnings generated.
2537:info:build In file included from clustalW/multipleAlign/Iteration.cpp:13:
2538:info:build In file included from clustalW/multipleAlign/Iteration.h:8:
2539:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2540:info:build In file included from clustalW/alignment/Sequence.h:20:
2541:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2542:info:build In file included from clustalW/general/UserParameters.h:22:
2543:info:build In file included from clustalW/general/utils.h:8:
2544:info:build In file included from clustalW/general/Utility.h:15:
2545:info:build In file included from clustalW/general/clustalw.h:44:
2546:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2547:info:build         int firstSeq, numSeqsInSub;
2548:info:build             ^
2549:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9:
2550:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13:
2551:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:42:
2552:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
2553:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2554:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
2555:info:build                                                              ^
2556:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2557:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
2558:info:build                                                                  ^
2559:info:build In file included from clustalW/multipleAlign/MSA.cpp:16:
2560:info:build In file included from clustalW/multipleAlign/MSA.h:10:
2561:info:build In file included from clustalW/multipleAlign/ProfileBase.h:14:
2562:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:42:
2563:info:build In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:
2564:info:build clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2565:info:build         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
2566:info:build                                                              ^
2567:info:build clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
2568:info:build         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
2569:info:build                                                                  ^
2570:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.cpp:9:
2571:info:build In file included from clustalW/multipleAlign/LowScoreSegProfile.h:13:
2572:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2573:info:build In file included from clustalW/alignment/Sequence.h:20:
2574:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2575:info:build In file included from clustalW/general/UserParameters.h:22:
2576:info:build In file included from clustalW/general/utils.h:8:
2577:info:build In file included from clustalW/general/Utility.h:15:
2578:info:build In file included from clustalW/general/clustalw.h:44:
2579:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2580:info:build         int firstSeq, numSeqsInSub;
2581:info:build             ^
2582:info:build clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
2583:info:build       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
2584:info:build           ^
2585:info:build clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter]
2586:info:build                            string phylipName)
2587:info:build                                   ^
2588:info:build In file included from clustalW/interface/CommandLineParser.cpp:13:
2589:info:build In file included from clustalW/interface/CommandLineParser.h:18:
2590:info:build In file included from clustalW/interface/../Clustal.h:15:
2591:info:build In file included from clustalW/general/clustalw.h:44:
2592:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2593:info:build         int firstSeq, numSeqsInSub;
2594:info:build             ^
2595:info:build In file included from clustalW/multipleAlign/MSA.cpp:16:
2596:info:build In file included from clustalW/multipleAlign/MSA.h:10:
2597:info:build In file included from clustalW/multipleAlign/ProfileBase.h:14:
2598:info:build In file included from clustalW/multipleAlign/../alignment/Alignment.h:41:
2599:info:build In file included from clustalW/alignment/Sequence.h:20:
2600:info:build In file included from clustalW/alignment/../general/userparams.h:8:
2601:info:build In file included from clustalW/general/UserParameters.h:22:
2602:info:build In file included from clustalW/general/utils.h:8:
2603:info:build In file included from clustalW/general/Utility.h:15:
2604:info:build In file included from clustalW/general/clustalw.h:44:
2605:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2606:info:build         int firstSeq, numSeqsInSub;
2607:info:build             ^
2608:info:build In file included from clustalW/interface/InteractiveMenu.cpp:23:
2609:info:build In file included from clustalW/interface/InteractiveMenu.h:15:
2610:info:build In file included from clustalW/interface/../Clustal.h:15:
2611:info:build In file included from clustalW/general/clustalw.h:44:
2612:info:build clustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
2613:info:build         int firstSeq, numSeqsInSub;
2614:info:build             ^
2615:info:build 5 warnings generated.
2616:info:build 7 warnings generated.
2617:info:build 5 warnings generated.
2618:info:build 6 warnings generated.
2619:info:build 5 warnings generated.
2620: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'
2621: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
2622:info:build Exit code: 2
2623:error:build org.macports.build for port clustalx returned: command execution failed
2624:debug:build Error code: CHILDSTATUS 18287 2
2625:debug:build Backtrace: command execution failed
2626    while executing
2627"system -nice 0 $fullcmdstring"
2628    ("eval" body line 1)
2629    invoked from within
2630"eval system $notty $nice \$fullcmdstring"
2631    invoked from within
2632"command_exec build"
2633    (procedure "portbuild::build_main" line 8)
2634    invoked from within
2635"$procedure $targetname"
2636:info:build Warning: targets not executed for clustalx: org.macports.activate org.macports.build org.macports.destroot org.macports.install
2637:notice:build Please see the log file for port clustalx for details:
2638    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/main.log