------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> clustalw-2.1_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> clustalw-2.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by clustalw-2.1_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> clustalw-2.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by clustalw-2.1_2 for building => SHA256 Checksum OK for clustalw-2.1.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> clustalw-2.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by clustalw-2.1_2 for building ===> Extracting for clustalw-2.1_2 => SHA256 Checksum OK for clustalw-2.1.tar.gz. Extracted Memory Use: 1.91M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for clustalw-2.1_2 ===> Applying ports patches for clustalw-2.1_2 from /xports/biology/clustalw/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> Configuring for clustalw-2.1_2 configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 checking target system type... x86_64-portbld-dragonfly5.9 configure: WARNING: "Couldn't determine target operating system. Using Unix" building for dragonfly5.9 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for clustalw-2.1_2 --- all-recursive --- Making all in m4 Making all in src --- all --- /usr/bin/make all-recursive --- all-recursive --- --- FullPairwiseAlign.o --- --- FastPairwiseAlign.o --- --- MSFFileParser.o --- --- FileReader.o --- --- PIRFileParser.o --- --- RSFFileParser.o --- --- GDEFileParser.o --- --- InFileStream.o --- --- ClustalFileParser.o --- --- PearsonFileParser.o --- --- FullPairwiseAlign.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FullPairwiseAlign.o -MD -MP -MF .deps/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp --- FastPairwiseAlign.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FastPairwiseAlign.o -MD -MP -MF .deps/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp --- MSFFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT MSFFileParser.o -MD -MP -MF .deps/MSFFileParser.Tpo -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp --- FileReader.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FileReader.o -MD -MP -MF .deps/FileReader.Tpo -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp --- PIRFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT PIRFileParser.o -MD -MP -MF .deps/PIRFileParser.Tpo -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp --- GDEFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT GDEFileParser.o -MD -MP -MF .deps/GDEFileParser.Tpo -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp --- ClustalFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClustalFileParser.o -MD -MP -MF .deps/ClustalFileParser.Tpo -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp --- PearsonFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT PearsonFileParser.o -MD -MP -MF .deps/PearsonFileParser.Tpo -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp --- RSFFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RSFFileParser.o -MD -MP -MF .deps/RSFFileParser.Tpo -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp --- InFileStream.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT InFileStream.o -MD -MP -MF .deps/InFileStream.Tpo -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp --- FastPairwiseAlign.o --- In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FastPairwiseAlign.h:9, from ./pairwise/FastPairwiseAlign.cpp:10: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- FullPairwiseAlign.o --- In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FullPairwiseAlign.h:9, from ./pairwise/FullPairwiseAlign.cpp:9: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- FileReader.o --- In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./fileInput/FileReader.cpp:29: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./fileInput/FileReader.cpp:29: ./fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::__cxx11::string*)': ./fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fileParser; // Means we dont need to delete it! ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./fileInput/FileReader.cpp: At global scope: ./fileInput/FileReader.cpp:426:42: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- InFileStream.o --- mv -f .deps/InFileStream.Tpo .deps/InFileStream.Po --- FileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FileParser.o -MD -MP -MF .deps/FileParser.Tpo -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp --- FullPairwiseAlign.o --- mv -f .deps/FullPairwiseAlign.Tpo .deps/FullPairwiseAlign.Po --- EMBLFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT EMBLFileParser.o -MD -MP -MF .deps/EMBLFileParser.Tpo -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp --- MSFFileParser.o --- mv -f .deps/MSFFileParser.Tpo .deps/MSFFileParser.Po --- RootedClusterTree.o --- --- FastPairwiseAlign.o --- mv -f .deps/FastPairwiseAlign.Tpo .deps/FastPairwiseAlign.Po --- RootedClusterTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RootedClusterTree.o -MD -MP -MF .deps/RootedClusterTree.Tpo -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp --- UPGMAAlgorithm.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT UPGMAAlgorithm.o -MD -MP -MF .deps/UPGMAAlgorithm.Tpo -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp --- RSFFileParser.o --- mv -f .deps/RSFFileParser.Tpo .deps/RSFFileParser.Po --- Node.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Node.o -MD -MP -MF .deps/Node.Tpo -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp --- PIRFileParser.o --- mv -f .deps/PIRFileParser.Tpo .deps/PIRFileParser.Po --- RootedGuideTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RootedGuideTree.o -MD -MP -MF .deps/RootedGuideTree.Tpo -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp --- GDEFileParser.o --- mv -f .deps/GDEFileParser.Tpo .deps/GDEFileParser.Po --- RootedTreeOutput.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RootedTreeOutput.o -MD -MP -MF .deps/RootedTreeOutput.Tpo -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp --- PearsonFileParser.o --- mv -f .deps/PearsonFileParser.Tpo .deps/PearsonFileParser.Po --- Tree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Tree.o -MD -MP -MF .deps/Tree.Tpo -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp --- ClustalFileParser.o --- mv -f .deps/ClustalFileParser.Tpo .deps/ClustalFileParser.Po --- ClusterTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClusterTree.o -MD -MP -MF .deps/ClusterTree.Tpo -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp --- FileParser.o --- mv -f .deps/FileParser.Tpo .deps/FileParser.Po --- TreeInterface.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT TreeInterface.o -MD -MP -MF .deps/TreeInterface.Tpo -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp --- FileReader.o --- mv -f .deps/FileReader.Tpo .deps/FileReader.Po --- UnRootedClusterTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT UnRootedClusterTree.o -MD -MP -MF .deps/UnRootedClusterTree.Tpo -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp --- RootedGuideTree.o --- In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedGuideTree.cpp:10: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- RootedClusterTree.o --- In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/../ClusterTree.h:20, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ClusterTree.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/ClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- RootedClusterTree.o --- In file included from ./tree/UPGMA/../ClusterTree.h:23, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- ClusterTree.o --- In file included from ./tree/ClusterTree.h:23, from ./tree/ClusterTree.cpp:9: ./tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/ClusterTree.cpp:9: ./tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- RootedClusterTree.o --- In file included from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTree(RootedGuideTree* phyTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- UPGMAAlgorithm.o --- In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/UPGMAAlgorithm.h:8, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- RootedClusterTree.o --- In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string&)': ./tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- UPGMAAlgorithm.o --- In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTree(RootedGuideTree* phyTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- Tree.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- RootedTreeOutput.o --- In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedTreeOutput.h:15, from ./tree/UPGMA/RootedTreeOutput.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- Tree.o --- In file included from ./tree/Tree.cpp:10: ./tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr createSets(int firstSeq, int lastSeq); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr Tree::createSets(int firstSeq, int lastSeq) ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/Tree.cpp: In member function 'std::auto_ptr clustalw::Tree::createSets(int, int)': ./tree/Tree.cpp:280:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progAlignSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- Node.o --- mv -f .deps/Node.Tpo .deps/Node.Po --- ClusterTreeOutput.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClusterTreeOutput.o -MD -MP -MF .deps/ClusterTreeOutput.Tpo -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp --- RootedGuideTree.o --- mv -f .deps/RootedGuideTree.Tpo .deps/RootedGuideTree.Po --- RandomGenerator.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RandomGenerator.o -MD -MP -MF .deps/RandomGenerator.Tpo -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp --- TreeInterface.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/TreeInterface.h:19, from ./tree/TreeInterface.cpp:15: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/ClusterTree.h:23, from ./tree/UnRootedClusterTree.h:8, from ./tree/TreeInterface.cpp:17: ./tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UnRootedClusterTree.h:8, from ./tree/TreeInterface.cpp:17: ./tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:18: ./tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr createSets(int firstSeq, int lastSeq); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- RandomGenerator.o --- mv -f .deps/RandomGenerator.Tpo .deps/RandomGenerator.Po --- NJTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT NJTree.o -MD -MP -MF .deps/NJTree.Tpo -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp --- TreeInterface.o --- In file included from ./tree/TreeInterface.cpp:23: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp:31:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp:103:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp:195:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': ./tree/TreeInterface.cpp:200:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:208:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::__cxx11::string*, std::vector*, int, int, bool*)': ./tree/TreeInterface.cpp:214:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:439:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::__cxx11::string*, std::vector*, int, int, bool*)': ./tree/TreeInterface.cpp:445:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:485:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': ./tree/TreeInterface.cpp:490:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:503:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': ./tree/TreeInterface.cpp:506:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- UnRootedClusterTree.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./tree/ClusterTree.h:23, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- EMBLFileParser.o --- mv -f .deps/EMBLFileParser.Tpo .deps/EMBLFileParser.Po --- AlignmentSteps.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT AlignmentSteps.o -MD -MP -MF .deps/AlignmentSteps.Tpo -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp --- RootedTreeOutput.o --- mv -f .deps/RootedTreeOutput.Tpo .deps/RootedTreeOutput.Po --- InteractiveMenu.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT InteractiveMenu.o -MD -MP -MF .deps/InteractiveMenu.Tpo -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp --- UPGMAAlgorithm.o --- mv -f .deps/UPGMAAlgorithm.Tpo .deps/UPGMAAlgorithm.Po --- CommandLineParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT CommandLineParser.o -MD -MP -MF .deps/CommandLineParser.Tpo -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp --- RootedClusterTree.o --- mv -f .deps/RootedClusterTree.Tpo .deps/RootedClusterTree.Po --- SubMatrix.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT SubMatrix.o -MD -MP -MF .deps/SubMatrix.Tpo -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp --- ClusterTreeOutput.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTreeOutput.h:11, from ./tree/ClusterTreeOutput.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- InteractiveMenu.o --- In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- SubMatrix.o --- In file included from ./substitutionMatrix/SubMatrix.cpp:15: ./substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- TreeInterface.o --- mv -f .deps/TreeInterface.Tpo .deps/TreeInterface.Po --- Iteration.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Iteration.o -MD -MP -MF .deps/Iteration.Tpo -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp --- AlignmentSteps.o --- mv -f .deps/AlignmentSteps.Tpo .deps/AlignmentSteps.Po --- MSA.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT MSA.o -MD -MP -MF .deps/MSA.Tpo -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp --- Tree.o --- mv -f .deps/Tree.Tpo .deps/Tree.Po --- MyersMillerProfileAlign.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT MyersMillerProfileAlign.o -MD -MP -MF .deps/MyersMillerProfileAlign.Tpo -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp --- ClusterTree.o --- mv -f .deps/ClusterTree.Tpo .deps/ClusterTree.Po --- ProfileStandard.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ProfileStandard.o -MD -MP -MF .deps/ProfileStandard.Tpo -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp --- InteractiveMenu.o --- In file included from ./interface/../Clustal.h:18, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- CommandLineParser.o --- In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./interface/../Clustal.h:18, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- ClusterTreeOutput.o --- mv -f .deps/ClusterTreeOutput.Tpo .deps/ClusterTreeOutput.Po --- ProfileWithSub.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ProfileWithSub.o -MD -MP -MF .deps/ProfileWithSub.Tpo -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp --- UnRootedClusterTree.o --- mv -f .deps/UnRootedClusterTree.Tpo .deps/UnRootedClusterTree.Po --- ProfileBase.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ProfileBase.o -MD -MP -MF .deps/ProfileBase.Tpo -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp --- MyersMillerProfileAlign.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileAlignAlgorithm.h:10, from ./multipleAlign/MyersMillerProfileAlign.h:10, from ./multipleAlign/MyersMillerProfileAlign.cpp:10: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- MSA.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/MSA.h:10, from ./multipleAlign/MSA.cpp:16: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- NJTree.o --- mv -f .deps/NJTree.Tpo .deps/NJTree.Po --- LowScoreSegProfile.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT LowScoreSegProfile.o -MD -MP -MF .deps/LowScoreSegProfile.Tpo -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp --- Iteration.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ProfileStandard.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileStandard.h:9, from ./multipleAlign/ProfileStandard.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- Iteration.o --- In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- ProfileWithSub.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileWithSub.h:9, from ./multipleAlign/ProfileWithSub.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ProfileBase.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/ProfileBase.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- InteractiveMenu.o --- mv -f .deps/InteractiveMenu.Tpo .deps/InteractiveMenu.Po --- OutputFile.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT OutputFile.o -MD -MP -MF .deps/OutputFile.Tpo -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp --- ProfileStandard.o --- mv -f .deps/ProfileStandard.Tpo .deps/ProfileStandard.Po --- UserParameters.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT UserParameters.o -MD -MP -MF .deps/UserParameters.Tpo -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp --- SubMatrix.o --- mv -f .deps/SubMatrix.Tpo .deps/SubMatrix.Po --- Utility.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Utility.o -MD -MP -MF .deps/Utility.Tpo -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp --- LowScoreSegProfile.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/LowScoreSegProfile.h:13, from ./multipleAlign/LowScoreSegProfile.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ProfileWithSub.o --- mv -f .deps/ProfileWithSub.Tpo .deps/ProfileWithSub.Po --- InvalidCombination.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT InvalidCombination.o -MD -MP -MF .deps/InvalidCombination.Tpo -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp --- OutputFile.o --- In file included from ./general/OutputFile.cpp:9: ./general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./general/OutputFile.h:8, from ./general/OutputFile.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- MSA.o --- mv -f .deps/MSA.Tpo .deps/MSA.Po --- DebugLog.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT DebugLog.o -MD -MP -MF .deps/DebugLog.Tpo -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp --- ProfileBase.o --- mv -f .deps/ProfileBase.Tpo .deps/ProfileBase.Po --- ClustalWResources.o --- --- LowScoreSegProfile.o --- mv -f .deps/LowScoreSegProfile.Tpo .deps/LowScoreSegProfile.Po --- ClustalWResources.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClustalWResources.o -MD -MP -MF .deps/ClustalWResources.Tpo -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp --- VectorOutOfRange.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT VectorOutOfRange.o -MD -MP -MF .deps/VectorOutOfRange.Tpo -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp --- InvalidCombination.o --- mv -f .deps/InvalidCombination.Tpo .deps/InvalidCombination.Po --- SymMatrix.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT SymMatrix.o -MD -MP -MF .deps/SymMatrix.Tpo -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp --- MyersMillerProfileAlign.o --- mv -f .deps/MyersMillerProfileAlign.Tpo .deps/MyersMillerProfileAlign.Po --- Stats.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp --- VectorOutOfRange.o --- mv -f .deps/VectorOutOfRange.Tpo .deps/VectorOutOfRange.Po --- Help.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Help.o -MD -MP -MF .deps/Help.Tpo -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp --- DebugLog.o --- mv -f .deps/DebugLog.Tpo .deps/DebugLog.Po --- Alignment.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Alignment.o -MD -MP -MF .deps/Alignment.Tpo -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp --- OutputFile.o --- mv -f .deps/OutputFile.Tpo .deps/OutputFile.Po --- AlignmentOutput.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT AlignmentOutput.o -MD -MP -MF .deps/AlignmentOutput.Tpo -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp --- UserParameters.o --- mv -f .deps/UserParameters.Tpo .deps/UserParameters.Po --- ObjectiveScore.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ObjectiveScore.o -MD -MP -MF .deps/ObjectiveScore.Tpo -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp --- SymMatrix.o --- mv -f .deps/SymMatrix.Tpo .deps/SymMatrix.Po --- Sequence.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Sequence.o -MD -MP -MF .deps/Sequence.Tpo -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp --- Utility.o --- mv -f .deps/Utility.Tpo .deps/Utility.Po --- Clustal.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Clustal.o -MD -MP -MF .deps/Clustal.Tpo -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp --- Iteration.o --- mv -f .deps/Iteration.Tpo .deps/Iteration.Po --- main.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp --- Stats.o --- In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./general/../alignment/Alignment.h:42, from ./general/Stats.cpp:15: ./general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- CommandLineParser.o --- mv -f .deps/CommandLineParser.Tpo .deps/CommandLineParser.Po --- ObjectiveScore.o --- In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/ObjectiveScore.h:15, from ./alignment/ObjectiveScore.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- Alignment.o --- In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./alignment/Alignment.cpp:25: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- Stats.o --- mv -f .deps/Stats.Tpo .deps/Stats.Po --- ClustalWResources.o --- mv -f .deps/ClustalWResources.Tpo .deps/ClustalWResources.Po --- Clustal.o --- In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::align(std::__cxx11::string*, bool)': ./Clustal.cpp:162:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- main.o --- In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./main.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- Clustal.o --- ./Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::__cxx11::string*)': ./Clustal.cpp:837:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- AlignmentOutput.o --- In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./alignment/AlignmentOutput.h:24, from ./alignment/AlignmentOutput.cpp:27: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./alignment/AlignmentOutput.cpp:512:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ./alignment/AlignmentOutput.cpp:535:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string AlignmentOutput::openOutputFile(auto_ptr& outFile, string prompt, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- main.o --- In file included from ./main.cpp:16: ./fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- Help.o --- mv -f .deps/Help.Tpo .deps/Help.Po --- ObjectiveScore.o --- mv -f .deps/ObjectiveScore.Tpo .deps/ObjectiveScore.Po --- Sequence.o --- mv -f .deps/Sequence.Tpo .deps/Sequence.Po --- main.o --- mv -f .deps/main.Tpo .deps/main.Po --- Alignment.o --- mv -f .deps/Alignment.Tpo .deps/Alignment.Po --- Clustal.o --- mv -f .deps/Clustal.Tpo .deps/Clustal.Po --- AlignmentOutput.o --- mv -f .deps/AlignmentOutput.Tpo .deps/AlignmentOutput.Po --- clustalw2 --- c++ -pipe -O2 -fno-strict-aliasing -o clustalw2 FullPairwiseAlign.o FastPairwiseAlign.o MSFFileParser.o FileReader.o PIRFileParser.o RSFFileParser.o GDEFileParser.o InFileStream.o ClustalFileParser.o PearsonFileParser.o FileParser.o EMBLFileParser.o RootedClusterTree.o UPGMAAlgorithm.o Node.o RootedGuideTree.o RootedTreeOutput.o Tree.o ClusterTree.o TreeInterface.o UnRootedClusterTree.o ClusterTreeOutput.o RandomGenerator.o NJTree.o AlignmentSteps.o InteractiveMenu.o CommandLineParser.o SubMatrix.o Iteration.o MSA.o MyersMillerProfileAlign.o ProfileStandard.o ProfileWithSub.o ProfileBase.o LowScoreSegProfile.o OutputFile.o UserParameters.o Utility.o InvalidCombination.o DebugLog.o ClustalWResources.o VectorOutOfRange.o SymMatrix.o Stats.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o Clustal.o main.o Iteration.o:Iteration.cpp:function clustalw::Iteration::removeFirstIterate(clustalw::Alignment*): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() SUCCEEDED 00:00:16 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for clustalw-2.1_2 ===> Generating temporary packing list Making install in m4 test -z "/usr/local/share/aclocal" || /bin/mkdir -p "/construction/biology/clustalw/stage/usr/local/share/aclocal" Making install in src test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/clustalw/stage/usr/local/bin" install -s -m 555 clustalw2 '/construction/biology/clustalw/stage/usr/local/bin' ln -sf clustalw2 /construction/biology/clustalw/stage/usr/local/bin/clustalw ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for clustalw-2.1_2 file sizes/checksums [2]: 0% file sizes/checksums [2]: 100% packing files [2]: 0% packing files [2]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:23