D: [iurt_root_command] chroot
warning: Found bdb_ro Packages database while attempting sqlite backend: using bdb_ro backend.
Installing /home/iurt/rpmbuild/SRPMS/clustalx-2.1-18.mga9.src.rpm
Building target platforms: aarch64
Building for target aarch64
Executing(%prep): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.0tIZ16
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ '[' 1 -eq 1 ']'
+ '[' 1 -eq 1 ']'
+ '[' 1 -eq 1 ']'
+ cd /home/iurt/rpmbuild/BUILD
+ rm -rf clustalx-2.1
+ /usr/bin/gzip -dc /home/iurt/rpmbuild/SOURCES/clustalx-2.1.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd clustalx-2.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ /usr/bin/cat /home/iurt/rpmbuild/SOURCES/clustalx-2.1-qt5.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.IsL89P
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ cd clustalx-2.1
+ '[' 1 -eq 1 ']'
+ '[' 1 -eq 1 ']'
+ /usr/lib64/qt5/bin/qmake libsuff=64 'QMAKE_CFLAGS=-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables' 'QMAKE_CXXFLAGS=-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables' 'QMAKE_LFLAGS= -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags' QMAKE_STRIP=
Info: creating stash file /home/iurt/rpmbuild/BUILD/clustalx-2.1/.qmake.stash
+ /usr/bin/make -O -j8 V=1 VERBOSE=1
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HardCodedColorScheme.h:8,
from ColorParameters.h:11,
from ColorParameters.cpp:1:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
ColorParameters.cpp: In member function 'QColor ColorParameters::getResidueColor(QChar, QChar)':
ColorParameters.cpp:160:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<residueColors>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
160 | for(i = 0; i < colorPar.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable]
174 | char temp = colorPar[i].consensusConditionList[j].toLatin1();
| ^~~~
ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable]
157 | char showRes = res.toLatin1();
| ^~~~~~~
ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable]
158 | char showCon = consensus.toLatin1();
| ^~~~~~~
ColorParameters.cpp: In member function 'int ColorParameters::getResidueColorNum(QChar, QChar)':
ColorParameters.cpp:197:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<residueColors>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
197 | for(i = 0; i < colorPar.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable]
211 | char temp = colorPar[i].consensusConditionList[j].toLatin1();
| ^~~~
ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable]
194 | char showRes = res.toLatin1();
| ^~~~~~~
ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable]
195 | char showCon = consensus.toLatin1();
| ^~~~~~~
ColorParameters.cpp: In member function 'void ColorParameters::printColorInfo()':
ColorParameters.cpp:229:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<QString, QColor> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
229 | for(int i = 0; i < colors.size(); i++)
| ~~^~~~~~~~~~~~~~~
ColorParameters.cpp: In member function 'int ColorParameters::getIndexOfColor(QColor)':
ColorParameters.cpp:238:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<QString, QColor> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
238 | for(int i = 0; i < colors.size(); i++)
| ~~^~~~~~~~~~~~~~~
ColorParameters.cpp: In member function 'QColor ColorParameters::getColorFromNum(int)':
ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<residueColors>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
251 | if(colorNum > 0 && colorNum - 1 < colorPar.size())
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp
In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
from AlignmentParameters.cpp:22:
clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)':
AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter]
48 | void AlignmentParameters::showEvent(QShowEvent* event)
| ~~~~~~~~~~~~^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp
ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment]
74 | // tr("colorrules not found in the parameter file, using\
| ^
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HardCodedColorScheme.h:8,
from ColorParameters.h:11,
from ColorFileXmlParser.h:9,
from ColorFileXmlParser.cpp:3:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)':
ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter]
85 | QTreeWidgetItem *parentItem)
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~
ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)':
ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter]
138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem)
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~
ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)':
ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter]
175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem)
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from BootstrapTreeDialog.h:11,
from BootstrapTreeDialog.cpp:18:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from BootstrapTreeDialog.cpp:18:
BootstrapTreeDialog.h:70:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::TreeNames> treeFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from BootstrapTreeDialog.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o AlignOutputFileNames.o AlignOutputFileNames.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from AlignOutputFileNames.h:10,
from AlignOutputFileNames.cpp:26:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from AlignOutputFileNames.cpp:26:
AlignOutputFileNames.h:106:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
106 | auto_ptr<clustalw::AlignmentFileNames> outFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from AlignOutputFileNames.cpp:16:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HardCodedColorScheme.h:8,
from HardCodedColorScheme.cpp:1:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from AlignmentViewerWidget.h:36,
from AlignmentViewerWidget.cpp:66:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from AlignmentViewerWidget.cpp:68:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentViewerWidget.cpp:63:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()':
AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
588 | for(i = 0; i < len && i < gapMask->size(); i++)
| ~~^~~~~~~~~~~~~~~~~
AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()':
AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
645 | for (i = 0; i < len && i < _secStructMask->size();i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
652 | for(i = 0; i < len && i < ssMask.size(); i++)
| ~~^~~~~~~~~~~~~~~
AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)':
AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter]
781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event )
| ~~~~~~~~~~~~~~~^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o AlignmentWidget.o AlignmentWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from AlignmentWidget.h:41,
from AlignmentWidget.cpp:49:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from AlignmentWidget.cpp:49:
AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)':
AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder]
170 | bool blackAndWhite;
| ^~~~~~~~~~~~~
AlignmentWidget.h:161:27: warning: 'std::vector<QPixmap, std::allocator<QPixmap> >* AlignmentWidget::selectedColoredRes' [-Wreorder]
161 | std::vector<QPixmap>* selectedColoredRes;
| ^~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder]
65 | AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent)
| ^~~~~~~~~~~~~~~
AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()':
AlignmentWidget.cpp:225:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
225 | for(unsigned int j = 0; j < lengthLongestSeq; j++)
| ~~^~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:235:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<QPixmap, std::allocator<QPixmap> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
235 | if(code >= 0 && code < conservationPixmaps->size())
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:268:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<QPixmap, std::allocator<QPixmap> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
268 | if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size())
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:280:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<QPixmap, std::allocator<QPixmap> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
280 | if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size())
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:291:86: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
291 | if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j)
| ~~~~~~~~~~~~~~~~~~~~~^~~
AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable]
215 | int codeForSpace = clustalw::userParameters->resIndex(
| ^~~~~~~~~~~~
AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()':
AlignmentWidget.cpp:333:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<QPixmap, std::allocator<QPixmap> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
333 | if(i < secStructPixmaps->size() && i < secStructInfo.size())
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:344:34: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
344 | fontMetrics.width(secStructInfo[i])/2,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from /usr/include/qt5/QtGui/QtGui:26,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:4,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentWidget.cpp:48:
/usr/include/qt5/QtGui/qfontmetrics.h:110:9: note: declared here
110 | int width(QChar) const;
| ^~~~~
AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)':
AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<QPixmap, std::allocator<QPixmap> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
569 | if(selectedRes >= selectedColoredRes->size())
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()':
AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
689 | for(int j = 1; j <= strongGroup.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:693:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
693 | for(int j = 1; j <= weakGroup.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:700:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
700 | if((i + _fRes - 1 < (*alignment)[j].size()) &&
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:701:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
701 | (i + _fRes - 1 < (*alignment)[_fSeq].size()))
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:725:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
725 | for(int k = 1; k <= strongGroup.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:737:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
737 | for(int k = 1; k <= weakGroup.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:760:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
760 | for(int k = 1; k <= strongGroup.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:771:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
771 | for(int k = 1; k <= weakGroup.size(); k++)
| ~~^~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D<int>*, ColorParameters*)':
AlignmentWidget.cpp:878:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
878 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq))
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()':
AlignmentWidget.cpp:927:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
927 | if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq))
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()':
AlignmentWidget.cpp:1039:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1039 | for(int j = 0; j < aminoAcid.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~
AlignmentWidget.cpp:1051:49: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
1051 | fontMetrics.width(currentChar)/2,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/qt5/QtGui/QtGui:26,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:4,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentWidget.cpp:48:
/usr/include/qt5/QtGui/qfontmetrics.h:110:9: note: declared here
110 | int width(QChar) const;
| ^~~~~
AlignmentWidget.cpp:1079:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
1079 | fontMetrics.width(currentChar)/2,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/qt5/QtGui/QtGui:26,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:4,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentWidget.cpp:48:
/usr/include/qt5/QtGui/qfontmetrics.h:110:9: note: declared here
110 | int width(QChar) const;
| ^~~~~
AlignmentWidget.cpp:1089:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
1089 | fontMetrics.width(currentChar)/2,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/qt5/QtGui/QtGui:26,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:4,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentWidget.cpp:48:
/usr/include/qt5/QtGui/qfontmetrics.h:110:9: note: declared here
110 | int width(QChar) const;
| ^~~~~
AlignmentWidget.cpp:1099:45: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
1099 | fontMetrics.width(currentChar)/2,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/qt5/QtGui/QtGui:26,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:4,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentWidget.cpp:48:
/usr/include/qt5/QtGui/qfontmetrics.h:110:9: note: declared here
110 | int width(QChar) const;
| ^~~~~
AlignmentWidget.cpp:1118:30: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
1118 | fontMetrics.width(currentChar)/2,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/qt5/QtGui/QtGui:26,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:4,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from AlignmentWidget.cpp:48:
/usr/include/qt5/QtGui/qfontmetrics.h:110:9: note: declared here
110 | int width(QChar) const;
| ^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp
In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
from ColumnScoreParams.cpp:23:
clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)':
ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter]
51 | void ColumnScoreParams::showEvent(QShowEvent* event)
| ~~~~~~~~~~~~^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from PostscriptFileParams.h:4,
from PostscriptFileParams.cpp:1:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o main.o main.cpp
In file included from main.cpp:21:
clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/Clustal.h:18,
from mainwindow.h:45,
from main.cpp:24:
clustalW/fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from main.cpp:24:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/substitutionMatrix/../general/SquareMat.h:9,
from clustalW/substitutionMatrix/../general/clustalw.h:43,
from clustalW/substitutionMatrix/SubMatrix.h:28,
from main.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HelpDisplayWidget.h:18,
from HelpDisplayWidget.cpp:15:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
HelpDisplayWidget.cpp: In member function 'std::string* HelpDisplayWidget::loadHelpInformation(char)':
HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
147 | catch(ifstream::failure e)
| ^
HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable]
61 | int i, number, nlines;
| ^~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp
HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)':
HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
180 | if(column >= 0 && column < arrayOfHeights->size())
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
198 | if(column >= 0 && column < arrayOfHeights->size())
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
HistogramWidget.cpp:208:47: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
208 | (fontMetrics.width(QString::number(rulerNum))) / 2;
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/qt5/QtWidgets/qwidget.h:50,
from /usr/include/qt5/QtWidgets/qframe.h:44,
from /usr/include/qt5/QtWidgets/qlabel.h:44,
from /usr/include/qt5/QtWidgets/QLabel:1,
from HistogramWidget.h:29,
from HistogramWidget.cpp:23:
/usr/include/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
106 | int width(const QString &, int len = -1) const;
| ^~~~~
HistogramWidget.cpp:241:61: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
241 | (fontMetrics.width(QString::number(0))) / 2, yPos, boxWidth,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/qt5/QtWidgets/qwidget.h:50,
from /usr/include/qt5/QtWidgets/qframe.h:44,
from /usr/include/qt5/QtWidgets/qlabel.h:44,
from /usr/include/qt5/QtWidgets/QLabel:1,
from HistogramWidget.h:29,
from HistogramWidget.cpp:23:
/usr/include/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
106 | int width(const QString &, int len = -1) const;
| ^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp
In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
from LowScoringSegParams.cpp:22:
clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)':
LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter]
51 | void LowScoringSegParams::showEvent(QShowEvent* event)
| ~~~~~~~~~~~~^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp
In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
from PairwiseParams.cpp:23:
clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
PairwiseParams.cpp: In member function 'virtual void PairwiseParams::showEvent(QShowEvent*)':
PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter]
74 | void PairwiseParams::showEvent(QShowEvent* event)
| ~~~~~~~~~~~~^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HardCodedColorScheme.h:8,
from ColorParameters.h:11,
from PSPrinter.h:11,
from PSPrinter.cpp:20:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)':
PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
207 | if(res.isLetter() && resNumber.size() > i - data->firstSeq)
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
307 | if(res.isLetter() && resNumber.size() > seq)
| ~~~~~~~~~~~~~~~~~^~~~~
PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
421 | if(res.isLetter() && resNumber.size() > i)
| ~~~~~~~~~~~~~~~~~^~~
PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable]
55 | int err;
| ^~~
PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable]
73 | int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local
| ^~~~~~~
PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable]
74 | int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local
| ^~~~~~~
PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)':
PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector<QString>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
587 | if(data->nameHeader.size() > ix)
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)':
PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
730 | for(i = fr; i <= lr && i < ruler.length(); i++)
| ~~^~~~~~~~~~~~~~~~
PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)':
PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
789 | for(i = fr + 1; i <= lr && i < data->histogram->size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable]
781 | int psX, psY, curveBottom;
| ^~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from AlignmentViewerWidget.h:36,
from mainwindow.h:37,
from mainwindow.cpp:98:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/Clustal.h:18,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from mainwindow.cpp:98:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from mainwindow.cpp:99:
WritePostscriptFile.h:88:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
88 | auto_ptr<PostscriptFileParams> params;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from mainwindow.cpp:100:
AlignOutputFileNames.h:106:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
106 | auto_ptr<clustalw::AlignmentFileNames> outFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from mainwindow.cpp:101:
TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
73 | auto_ptr<clustalw::TreeNames> treeFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from mainwindow.cpp:102:
BootstrapTreeDialog.h:70:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::TreeNames> treeFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtCore/qdebug.h:54,
from /usr/include/qt5/QtCore/qcborcommon.h:45,
from /usr/include/qt5/QtCore/qcborvalue.h:45,
from /usr/include/qt5/QtCore/qcborarray.h:43,
from /usr/include/qt5/QtCore/QtCore:38,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:3,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from mainwindow.cpp:90:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
mainwindow.cpp: In member function 'virtual void MainWindow::showEvent(QShowEvent*)':
mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter]
198 | void MainWindow::showEvent(QShowEvent* event)
| ~~~~~~~~~~~~^~~~~
mainwindow.cpp: In member function 'void MainWindow::writeViewer1AsPostscript(int)':
mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter]
1454 | void MainWindow::writeViewer1AsPostscript(int type)
| ~~~~^~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from SaveSeqFile.h:9,
from SaveSeqFile.cpp:23:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from SaveSeqFile.cpp:26:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from SaveSeqFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from SeqNameWidget.h:41,
from SeqNameWidget.cpp:59:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)':
SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable]
375 | QRect redrawRect = event->rect();
| ^~~~~~~~~~
SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()':
SeqNameWidget.cpp:443:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
443 | int length = fontMetrics.width(QString(name.c_str()));
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/qt5/QtGui/QtGui:26,
from /usr/include/qt5/QtWidgets/QtWidgetsDepends:4,
from /usr/include/qt5/QtWidgets/QtWidgets:3,
from SeqNameWidget.cpp:58:
/usr/include/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
106 | int width(const QString &, int len = -1) const;
| ^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/ObjectiveScore.h:15,
from clustalW/alignment/ObjectiveScore.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from TreeOutputFileNames.h:10,
from TreeOutputFileNames.cpp:17:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from TreeOutputFileNames.cpp:17:
TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
73 | auto_ptr<clustalw::TreeNames> treeFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from TreeOutputFileNames.cpp:7:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp
In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/fileInput/../alignment/Alignment.h:42,
from clustalW/fileInput/FileReader.h:12,
from clustalW/Clustal.h:18,
from clustalW/Clustal.cpp:27:
clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/Clustal.h:18,
from clustalW/Clustal.cpp:27:
clustalW/fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from clustalW/Clustal.cpp:27:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.cpp:33:
clustalW/tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
38 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.cpp:33:
clustalW/tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
57 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.cpp:33:
clustalW/tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
102 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.cpp:33:
clustalW/tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
108 | auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.cpp:33:
clustalW/tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
133 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.cpp:33:
clustalW/tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
138 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.cpp:33:
clustalW/tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
142 | auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/Clustal.cpp: In member function 'void clustalw::Clustal::align(std::string*, bool)':
clustalW/Clustal.cpp:162:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
162 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::string*)':
clustalW/Clustal.cpp:837:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
837 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/general/SquareMat.h:9,
from clustalW/general/clustalw.h:43,
from clustalW/Clustal.h:15,
from clustalW/Clustal.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from WritePostscriptFile.h:10,
from WritePostscriptFile.cpp:24:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from WritePostscriptFile.cpp:24:
WritePostscriptFile.h:88:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
88 | auto_ptr<PostscriptFileParams> params;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from WritePostscriptFile.cpp:27:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from /usr/include/qt5/QtCore/qsharedpointer_impl.h:71,
from /usr/include/qt5/QtCore/qsharedpointer.h:48,
from /usr/include/qt5/QtGui/qpixmap.h:48,
from /usr/include/qt5/QtGui/qicon.h:46,
from /usr/include/qt5/QtWidgets/qabstractbutton.h:44,
from /usr/include/qt5/QtWidgets/qpushbutton.h:44,
from /usr/include/qt5/QtWidgets/QPushButton:1,
from WritePostscriptFile.cpp:14:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp
clustalW/fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()':
clustalW/fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
37 | register int i;
| ^
clustalW/fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
38 | register char c;
| ^
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from clustalW/alignment/Alignment.cpp:25:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()':
clustalW/alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
47 | register int sl; /* which have code = gap_pos2 */
| ^~
clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()':
clustalW/alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
122 | register int sl; /* which have code = gap_pos2 */
| ^~
clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()':
clustalW/alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
617 | register int sl;
| ^~
clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin();
| ^~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp
clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector<clustalw::Sequence> clustalw::MSFFileParser::getSeqRange(int, int, std::string*)':
clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
34 | vector<Sequence> MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq)
| ~~~~~~~~^~~~~~~~~~~~
clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual void clustalw::MSFFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
246 | void MSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter]
246 | void MSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter]
247 | string& secStructName, int &structPenalties, int length)
| ~~~~~~~~^~~~~~~~~~~~~
clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter]
247 | string& secStructName, int &structPenalties, int length)
| ~~~~^~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp
In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/fileInput/../alignment/Alignment.h:42,
from clustalW/fileInput/FileReader.h:12,
from clustalW/fileInput/FileReader.cpp:29:
clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/fileInput/FileReader.cpp:29:
clustalW/fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/fileInput/FileReader.h:11,
from clustalW/fileInput/FileReader.cpp:29:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)':
clustalW/fileInput/FileReader.cpp:155:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
155 | auto_ptr<FileParser> fileParser; // Means we dont need to delete it!
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/fileInput/FileReader.h:11,
from clustalW/fileInput/FileReader.cpp:29:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/fileInput/FileReader.cpp: At global scope:
clustalW/fileInput/FileReader.cpp:426:42: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
426 | void FileReader::checkInfile(int *nseqs, auto_ptr<FileParser>& fileParser)
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/fileInput/FileReader.h:11,
from clustalW/fileInput/FileReader.cpp:29:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr<clustalw::FileParser>&)':
clustalW/fileInput/FileReader.cpp:555:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
555 | catch(exception ex)
| ^~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp
clustalW/fileInput/PIRFileParser.cpp: In member function 'virtual void clustalw::PIRFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
292 | void PIRFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter 'secStructMask' [-Wunused-parameter]
292 | void PIRFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter 'secStructName' [-Wunused-parameter]
293 | string& secStructName, int &structPenalties, int length)
| ~~~~~~~~^~~~~~~~~~~~~
clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter]
293 | string& secStructName, int &structPenalties, int length)
| ~~~~^~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp
clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::string*)':
clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
199 | Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq)
| ~~~~~~~~^~~~~~~~~~~~
clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
444 | void PearsonFileParser::getSecStructure(vector<char>& gapPenaltyMask,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter]
445 | vector<char>& secStructMask, string& secStructName,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter]
445 | vector<char>& secStructMask, string& secStructName,
| ~~~~~~~~^~~~~~~~~~~~~
clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter]
446 | int &structPenalties, int length)
| ~~~~^~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp
clustalW/general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const':
clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript 1 is above array bounds of 'char [1]' [-Warray-bounds]
106 | delim[1] = 0;
| ~~~~~~~^
clustalW/general/ClustalWResources.cpp:104:10: note: while referencing 'delim'
104 | char delim[1];
| ^~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp
clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
240 | void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from clustalW/alignment/AlignmentOutput.h:24,
from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/alignment/AlignmentOutput.cpp:27:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/alignment/AlignmentOutput.cpp:512:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
512 | bool AlignmentOutput::openExplicitFile(auto_ptr<ofstream>& outFile, string fileName)
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/alignment/AlignmentOutput.cpp:535:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
535 | string AlignmentOutput::openOutputFile(auto_ptr<ofstream>& outFile, string prompt,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/alignment/AlignmentOutput.h:20,
from clustalW/alignment/AlignmentOutput.cpp:27:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion)':
clustalW/alignment/AlignmentOutput.cpp:673:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
673 | catch(VectorOutOfRange e)
| ^
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)':
clustalW/alignment/AlignmentOutput.cpp:868:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
868 | catch(VectorOutOfRange e)
| ^
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)':
clustalW/alignment/AlignmentOutput.cpp:1027:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
1027 | catch(VectorOutOfRange e)
| ^
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)':
clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
1156 | catch(VectorOutOfRange e)
| ^
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)':
clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
1445 | catch(VectorOutOfRange e)
| ^
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)':
clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
1560 | catch(VectorOutOfRange e)
| ^
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)':
clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
2095 | catch(VectorOutOfRange e)
| ^
clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
2102 | catch(exception e)
| ^
clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)':
clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
2351 | catch(VectorOutOfRange e)
| ^
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp
In file included from clustalW/general/OutputFile.cpp:9:
clustalW/general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/general/OutputFile.h:8,
from clustalW/general/OutputFile.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp
In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/general/../alignment/Alignment.h:42,
from clustalW/general/Stats.cpp:15:
clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp
clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)':
clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter]
33 | UserParameters::UserParameters(bool log)
| ~~~~~^~~
clustalW/general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)':
clustalW/general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
475 | register int i;
| ^
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp
clustalW/general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)':
clustalW/general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
53 | register int p;
| ^
clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
251 | int n;
| ^
clustalW/general/Utility.cpp: In member function 'virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)':
clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter]
519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj)
| ~~~~~~~~^~~~~~~~~~~~~
clustalW/general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)':
clustalW/general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
183 | fgets(line, MAXLINE, stdin);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
clustalW/general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)':
clustalW/general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
221 | fgets(line, MAXLINE, stdin);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp
In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/multipleAlign/../alignment/Alignment.h:42,
from clustalW/multipleAlign/LowScoreSegProfile.h:13,
from clustalW/multipleAlign/LowScoreSegProfile.cpp:9:
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp
In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/multipleAlign/../alignment/Alignment.h:42,
from clustalW/multipleAlign/ProfileBase.h:14,
from clustalW/multipleAlign/MSA.h:10,
from clustalW/multipleAlign/MSA.cpp:16:
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
340 | int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::seqsAlignToProfile(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, int, std::string)':
clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter]
359 | string phylipName)
| ~~~~~~~^~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp
In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/interface/../fileInput/../alignment/Alignment.h:42,
from clustalW/interface/../fileInput/FileReader.h:12,
from clustalW/interface/../Clustal.h:18,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/interface/../Clustal.h:18,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/InteractiveMenu.h:15,
from clustalW/interface/InteractiveMenu.cpp:23:
clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/InteractiveMenu.cpp:21:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()':
clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
41 | catch(bad_alloc)
| ^~~~~~~~~
clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()':
clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=]
520 | clustalObj->getHelp('C');
| ~~~~~~~~~~~~~~~~~~~^~~~~
clustalW/interface/InteractiveMenu.cpp:521:13: note: here
521 | case 'Q':
| ^~~~
clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()':
clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1190 | system(lin1.c_str());
| ~~~~~~^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp
In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/multipleAlign/../alignment/Alignment.h:42,
from clustalW/multipleAlign/ProfileStandard.h:9,
from clustalW/multipleAlign/ProfileStandard.cpp:9:
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp
In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/multipleAlign/../alignment/Alignment.h:42,
from clustalW/multipleAlign/ProfileBase.h:14,
from clustalW/multipleAlign/ProfileBase.cpp:9:
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/ProfileBase.cpp: In member function 'void clustalw::ProfileBase::calcResidueSpecificPen(clustalw::SeqArray*, std::vector<int>*)':
clustalW/multipleAlign/ProfileBase.cpp:372:25: warning: comparison is always false due to limited range of data type [-Wtype-limits]
372 | if ((ix < 0) || (ix > _maxAA))
| ~~~^~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp
In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/multipleAlign/../alignment/Alignment.h:42,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/multipleAlign/Iteration.cpp:17:
clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
38 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/multipleAlign/../alignment/Alignment.h:38,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/multipleAlign/Iteration.cpp:17:
clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
57 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/multipleAlign/../alignment/Alignment.h:38,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/multipleAlign/Iteration.cpp:17:
clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
102 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/multipleAlign/../alignment/Alignment.h:38,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/multipleAlign/Iteration.cpp:17:
clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
108 | auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/multipleAlign/../alignment/Alignment.h:38,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/multipleAlign/Iteration.cpp:17:
clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
133 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/multipleAlign/../alignment/Alignment.h:38,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/multipleAlign/Iteration.cpp:17:
clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
138 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/multipleAlign/../alignment/Alignment.h:38,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/multipleAlign/Iteration.cpp:17:
clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
142 | auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/multipleAlign/../alignment/Alignment.h:38,
from clustalW/multipleAlign/Iteration.h:8,
from clustalW/multipleAlign/Iteration.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
170 | int count;
| ^~~~~
clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | tmpnam (buffer);
| ~~~~~~~^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp
In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/multipleAlign/../alignment/Alignment.h:42,
from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10,
from clustalW/multipleAlign/MyersMillerProfileAlign.h:10,
from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10:
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp
In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/multipleAlign/../alignment/Alignment.h:42,
from clustalW/multipleAlign/ProfileWithSub.h:9,
from clustalW/multipleAlign/ProfileWithSub.cpp:9:
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp
In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/pairwise/../alignment/Alignment.h:42,
from clustalW/pairwise/PairwiseAlignBase.h:10,
from clustalW/pairwise/FastPairwiseAlign.h:9,
from clustalW/pairwise/FastPairwiseAlign.cpp:10:
clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp
In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/pairwise/../alignment/Alignment.h:42,
from clustalW/pairwise/PairwiseAlignBase.h:10,
from clustalW/pairwise/FullPairwiseAlign.h:9,
from clustalW/pairwise/FullPairwiseAlign.cpp:9:
clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp
In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/../alignment/Alignment.h:42,
from clustalW/tree/ClusterTreeOutput.h:11,
from clustalW/tree/ClusterTreeOutput.cpp:9:
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp
clustalW/tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)':
clustalW/tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
164 | register int i;
| ^
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp
In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/interface/../fileInput/../alignment/Alignment.h:42,
from clustalW/interface/../fileInput/FileReader.h:12,
from clustalW/interface/../Clustal.h:18,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/interface/../Clustal.h:18,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/interface/../Clustal.h:20,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/interface/../general/SquareMat.h:9,
from clustalW/interface/../general/clustalw.h:43,
from clustalW/interface/../Clustal.h:15,
from clustalW/interface/CommandLineParser.h:18,
from clustalW/interface/CommandLineParser.cpp:13:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp
In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/../alignment/Alignment.h:42,
from clustalW/tree/ClusterTree.h:20,
from clustalW/tree/ClusterTree.cpp:9:
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/tree/ClusterTree.h:23,
from clustalW/tree/ClusterTree.cpp:9:
clustalW/tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/ClusterTree.h:16,
from clustalW/tree/ClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/ClusterTree.cpp:9:
clustalW/tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/ClusterTree.h:16,
from clustalW/tree/ClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
580 | int rs = 0, rl = 0;
| ^~
clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
580 | int rs = 0, rl = 0;
| ^~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp
In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15:
clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::tempInterface(int, int)':
clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter 'alignResidueType' [-Wunused-parameter]
1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType)
| ~~~~^~~~~~~~~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.cpp:1613:57: warning: unused parameter 'alignType' [-Wunused-parameter]
1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType)
| ~~~~^~~~~~~~~
clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
1657 | int maxRes;
| ^~~~~~
clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
1717 | int maxRes;
| ^~~~~~
clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized]
1103 | return (maxRes);
| ^
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp
In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/../alignment/Alignment.h:42,
from clustalW/tree/Tree.h:13,
from clustalW/tree/Tree.cpp:10:
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/tree/Tree.cpp:10:
clustalW/tree/Tree.h:26:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/tree/../alignment/Alignment.h:38,
from clustalW/tree/Tree.h:13,
from clustalW/tree/Tree.cpp:10:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/Tree.cpp:278:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
278 | auto_ptr<AlignmentSteps> Tree::createSets(int firstSeq, int lastSeq)
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/tree/../alignment/Alignment.h:38,
from clustalW/tree/Tree.h:13,
from clustalW/tree/Tree.cpp:10:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/Tree.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::Tree::createSets(int, int)':
clustalW/tree/Tree.cpp:280:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
280 | auto_ptr<AlignmentSteps> progAlignSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/tree/../alignment/Alignment.h:38,
from clustalW/tree/Tree.h:13,
from clustalW/tree/Tree.cpp:10:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib64/qt5/mkspecs/features/data/dummy.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp
In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/../alignment/Alignment.h:42,
from clustalW/tree/TreeInterface.h:19,
from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
38 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
57 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
102 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
108 | auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
133 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
138 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:15:
clustalW/tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
142 | auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/ClusterTree.h:23,
from clustalW/tree/UnRootedClusterTree.h:8,
from clustalW/tree/TreeInterface.cpp:17:
clustalW/tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/UnRootedClusterTree.h:8,
from clustalW/tree/TreeInterface.cpp:17:
clustalW/tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:18:
clustalW/tree/Tree.h:26:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/TreeInterface.cpp:23:
clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
22 | auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp:31:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp:103:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
103 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp:195:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
195 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector<int>*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)':
clustalW/tree/TreeInterface.cpp:200:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
200 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: At global scope:
clustalW/tree/TreeInterface.cpp:208:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
208 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::string*, std::vector<int>*, int, int, bool*)':
clustalW/tree/TreeInterface.cpp:214:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
214 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: At global scope:
clustalW/tree/TreeInterface.cpp:439:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
439 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::string*, std::vector<int>*, int, int, bool*)':
clustalW/tree/TreeInterface.cpp:445:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
445 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: At global scope:
clustalW/tree/TreeInterface.cpp:485:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
485 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector<int>*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)':
clustalW/tree/TreeInterface.cpp:490:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
490 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: At global scope:
clustalW/tree/TreeInterface.cpp:503:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
503 | auto_ptr<AlignmentSteps> TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)':
clustalW/tree/TreeInterface.cpp:506:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
506 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/TreeInterface.h:17,
from clustalW/tree/TreeInterface.cpp:15:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp
In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
from clustalW/tree/UPGMA/RootedGuideTree.h:17,
from clustalW/tree/UPGMA/RootedTreeOutput.h:15,
from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9:
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp
In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
from clustalW/tree/UPGMA/RootedGuideTree.h:17,
from clustalW/tree/UPGMA/RootedGuideTree.cpp:10:
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include FileDialog.h -o moc_FileDialog.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include HistogramWidget.h -o moc_HistogramWidget.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include LowScoringSegParams.h -o moc_LowScoringSegParams.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include mainwindow.h -o moc_mainwindow.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp
In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
from clustalW/tree/UPGMA/../ClusterTree.h:20,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/tree/UPGMA/../ClusterTree.h:23,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
clustalW/tree/UPGMA/../../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/UPGMA/../ClusterTree.h:16,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
clustalW/tree/UPGMA/../ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/UPGMA/../ClusterTree.h:16,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
22 | auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/UPGMA/../ClusterTree.h:16,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11:
clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
23 | auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/UPGMA/../ClusterTree.h:16,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11:
clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
51 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/UPGMA/../ClusterTree.h:16,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
17 | auto_ptr<AlignmentSteps> RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/UPGMA/../ClusterTree.h:16,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
clustalW/tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
21 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/UPGMA/../ClusterTree.h:16,
from clustalW/tree/UPGMA/RootedClusterTree.h:8,
from clustalW/tree/UPGMA/RootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include PSPrinter.h -o moc_PSPrinter.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp
In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/../alignment/Alignment.h:42,
from clustalW/tree/ClusterTree.h:20,
from clustalW/tree/UnRootedClusterTree.h:8,
from clustalW/tree/UnRootedClusterTree.cpp:9:
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/tree/ClusterTree.h:23,
from clustalW/tree/UnRootedClusterTree.h:8,
from clustalW/tree/UnRootedClusterTree.cpp:9:
clustalW/tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/ClusterTree.h:16,
from clustalW/tree/UnRootedClusterTree.h:8,
from clustalW/tree/UnRootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/UnRootedClusterTree.h:8,
from clustalW/tree/UnRootedClusterTree.cpp:9:
clustalW/tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from clustalW/tree/ClusterTree.h:16,
from clustalW/tree/UnRootedClusterTree.h:8,
from clustalW/tree/UnRootedClusterTree.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include SearchForString.h -o moc_SearchForString.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include SecStructOptions.h -o moc_SecStructOptions.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include TreeFormatOptions.h -o moc_TreeFormatOptions.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include SeqNameWidget.h -o moc_SeqNameWidget.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp
/usr/lib64/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /home/iurt/rpmbuild/BUILD/clustalx-2.1/moc_predefs.h -I/usr/lib64/qt5/mkspecs/linux-g++ -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1 -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/general -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/substitutionMatrix -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/alignment -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/fileInput -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/interface -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/pairwise -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree -I/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I/usr/include/c++/11 -I/usr/include/c++/11/aarch64-mageia-linux -I/usr/include/c++/11/backward -I/usr/lib/gcc/aarch64-mageia-linux/11/include -I/usr/local/include -I/usr/include WritePostscriptFile.h -o moc_WritePostscriptFile.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp
In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
from clustalW/tree/UPGMA/RootedGuideTree.h:17,
from clustalW/tree/UPGMA/UPGMAAlgorithm.h:8,
from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
23 | auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/tree/UPGMA/../../general/SquareMat.h:9,
from clustalW/tree/UPGMA/../../general/clustalw.h:43,
from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6,
from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
51 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/tree/UPGMA/../../general/SquareMat.h:9,
from clustalW/tree/UPGMA/../../general/clustalw.h:43,
from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6,
from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
27 | auto_ptr<AlignmentSteps> UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree,
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from clustalW/tree/UPGMA/../../general/SquareMat.h:9,
from clustalW/tree/UPGMA/../../general/clustalw.h:43,
from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6,
from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from AlignmentViewerWidget.h:36,
from moc_AlignmentViewerWidget.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from BootstrapTreeDialog.h:11,
from moc_BootstrapTreeDialog.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from moc_BootstrapTreeDialog.cpp:10:
BootstrapTreeDialog.h:70:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::TreeNames> treeFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_BootstrapTreeDialog.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from AlignOutputFileNames.h:10,
from moc_AlignOutputFileNames.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from moc_AlignOutputFileNames.cpp:10:
AlignOutputFileNames.h:106:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
106 | auto_ptr<clustalw::AlignmentFileNames> outFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_AlignOutputFileNames.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from AlignmentWidget.h:41,
from moc_AlignmentWidget.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HardCodedColorScheme.h:8,
from ColorParameters.h:11,
from ColorFileXmlParser.h:9,
from moc_ColorFileXmlParser.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HelpDisplayWidget.h:18,
from moc_HelpDisplayWidget.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from HardCodedColorScheme.h:8,
from ColorParameters.h:11,
from PSPrinter.h:11,
from moc_PSPrinter.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from AlignmentViewerWidget.h:36,
from mainwindow.h:37,
from moc_mainwindow.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from clustalW/Clustal.h:18,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from clustalW/Clustal.h:20,
from mainwindow.h:45,
from moc_mainwindow.cpp:10:
clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_mainwindow.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from SaveSeqFile.h:9,
from moc_SaveSeqFile.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from SeqNameWidget.h:41,
from moc_SeqNameWidget.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from TreeOutputFileNames.h:10,
from moc_TreeOutputFileNames.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from moc_TreeOutputFileNames.cpp:10:
TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
73 | auto_ptr<clustalw::TreeNames> treeFileNames;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_TreeOutputFileNames.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fno-strict-aliasing -DPIC -fPIC -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/qt5 -I/usr/include/qt5/QtWidgets -I/usr/include/qt5/QtGui -I/usr/include/qt5/QtXml -I/usr/include/qt5/QtCore -I. -I/usr/lib64/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from WritePostscriptFile.h:10,
from moc_WritePostscriptFile.cpp:10:
clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from moc_WritePostscriptFile.cpp:10:
WritePostscriptFile.h:88:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
88 | auto_ptr<PostscriptFileParams> params;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from moc_WritePostscriptFile.cpp:9:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags -Wl,-O1 -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o /usr/lib64/libQt5Widgets.so /usr/lib64/libQt5Gui.so /usr/lib64/libQt5Xml.so /usr/lib64/libQt5Core.so -lGL -lpthread
/usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
/home/iurt/rpmbuild/BUILD/clustalx-2.1/clustalW/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.rRDawD
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ '[' 1 -eq 1 ']'
+ '[' /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64 '!=' / ']'
+ rm -rf /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64
++ dirname /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64
+ mkdir -p /home/iurt/rpmbuild/BUILDROOT
+ mkdir /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64
+ cd clustalx-2.1
+ '[' 1 -eq 1 ']'
+ /usr/bin/mkdir -p /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/clustalx
+ cp -a colprot.xml coldna.xml colprint.xml clustalx.hlp clustalx /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/clustalx/
+ /usr/bin/mkdir -p /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/bin
+ cat
+ chmod 755 /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/bin/clustalx
+ /usr/bin/install -d -m755 /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/applications
+ cat
+ /usr/bin/install -D -p -m644 /home/iurt/rpmbuild/SOURCES/clustalx.1 /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/man/man1/clustalx.1
+ /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 2.1-18.mga9 --unique-debug-suffix -2.1-18.mga9.aarch64 --unique-debug-src-base clustalx-2.1-18.mga9.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /home/iurt/rpmbuild/BUILD/clustalx-2.1
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/clustalx/clustalx
dwz: ./usr/share/clustalx/clustalx-2.1-18.mga9.aarch64.debug: Unknown debugging section .debug_line_str
original debug info size: 33472kB, size after compression: 33472kB
/usr/bin/sepdebugcrcfix: Updated 0 CRC32s, 1 CRC32s did match.
3196 blocks
+ /usr/lib/rpm/check-buildroot
+ '[' -n '' ']'
+ /usr/share/spec-helper/clean_files
+ '[' -n '' ']'
+ /usr/share/spec-helper/compress_files .xz
+ '[' -n '' ']'
+ /usr/share/spec-helper/relink_symlinks
+ '[' -n '' ']'
+ /usr/share/spec-helper/clean_perl
+ '[' -n '' ']'
+ /usr/share/spec-helper/lib_symlinks
+ '[' -n '' ']'
+ /usr/share/spec-helper/gprintify
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_mo
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_pamd
+ '[' -n '' ']'
+ /usr/share/spec-helper/remove_info_dir
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_eol
+ '[' -n '' ']'
+ /usr/share/spec-helper/check_desktop_files
+ '[' -n '' ']'
+ /usr/share/spec-helper/check_elf_files
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python3 1 0
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/clustalx from /bin/sh to #!/usr/bin/sh
Processing files: clustalx-2.1-18.mga9.aarch64
Executing(%doc): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.4Z120P
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ cd clustalx-2.1
+ DOCDIR=/home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/doc/clustalx
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/doc/clustalx
+ cp -pr COPYING /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/doc/clustalx
+ cp -pr COPYING.LESSER /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/doc/clustalx
+ cp -pr README /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64/usr/share/doc/clustalx
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: application() application(clustalx.desktop) clustalx = 2.1-18.mga9 clustalx(aarch-64) = 2.1-18.mga9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libQt5Core.so.5()(64bit) libQt5Core.so.5(Qt_5)(64bit) libQt5Gui.so.5()(64bit) libQt5Gui.so.5(Qt_5)(64bit) libQt5Widgets.so.5()(64bit) libQt5Widgets.so.5(Qt_5)(64bit) libQt5Xml.so.5()(64bit) libQt5Xml.so.5(Qt_5)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit)
Processing files: clustalx-debugsource-2.1-18.mga9.aarch64
Provides: clustalx-debugsource = 2.1-18.mga9 clustalx-debugsource(aarch-64) = 2.1-18.mga9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: clustalx-debuginfo-2.1-18.mga9.aarch64
Provides: clustalx-debuginfo = 2.1-18.mga9 clustalx-debuginfo(aarch-64) = 2.1-18.mga9 debuginfo(build-id) = ed78fc788d6499aed7c888150ed84e5ecb8ff73b
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: clustalx-debugsource(aarch-64) = 2.1-18.mga9
Checking for unpackaged file(s): /usr/lib/rpm/check-files /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64
Wrote: /home/iurt/rpmbuild/RPMS/aarch64/clustalx-2.1-18.mga9.aarch64.rpm
Wrote: /home/iurt/rpmbuild/RPMS/aarch64/clustalx-debugsource-2.1-18.mga9.aarch64.rpm
Wrote: /home/iurt/rpmbuild/RPMS/aarch64/clustalx-debuginfo-2.1-18.mga9.aarch64.rpm
Executing(%clean): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.NlH2uP
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ cd clustalx-2.1
+ /usr/bin/rm -rf /home/iurt/rpmbuild/BUILDROOT/clustalx-2.1-18.mga9.aarch64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(--clean): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.BlpXfT
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ rm -rf clustalx-2.1
+ RPM_EC=0
++ jobs -p
+ exit 0
D: [iurt_root_command] Success!