D: [iurt_root_command] chroot warning: Found bdb_ro Packages database while attempting sqlite backend: using bdb_ro backend. Installing /home/iurt/rpmbuild/SRPMS/clustalw-2.1-10.mga9.src.rpm Building target platforms: aarch64 Building for target aarch64 Executing(%prep): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.7Xyhl9 + umask 022 + cd /home/iurt/rpmbuild/BUILD + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + cd /home/iurt/rpmbuild/BUILD + rm -rf clustalw-2.1 + /usr/bin/gzip -dc /home/iurt/rpmbuild/SOURCES/clustalw-2.1.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd clustalw-2.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.ndoR44 + umask 022 + cd /home/iurt/rpmbuild/BUILD + cd clustalw-2.1 + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + autoreconf -vfi autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: running: /usr/bin/autoconf --force configure.ac:40: warning: The macro `AC_CANONICAL_SYSTEM' is obsolete. configure.ac:40: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:40: the top level configure.ac:90: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete. configure.ac:90: You should run autoupdate. ./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from... configure.ac:90: the top level configure.ac:94: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:94: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:94: the top level configure.ac:111: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:111: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:741: AM_CONFIG_HEADER is expanded from... configure.ac:111: the top level configure.ac:133: warning: AC_OUTPUT should be used without arguments. configure.ac:133: You should run autoupdate. autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:79: installing './compile' src/Makefile.am:21: warning: source file './pairwise/FullPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:21: warning: source file './pairwise/FastPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/MSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileReader.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PIRFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/RSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/GDEFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/InFileStream.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/ClustalFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PearsonFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/EMBLFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/UPGMAAlgorithm.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/Node.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedGuideTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/Tree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/TreeInterface.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UnRootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/RandomGenerator.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/NJTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/AlignmentSteps.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/InteractiveMenu.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/CommandLineParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './substitutionMatrix/SubMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/Iteration.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MSA.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MyersMillerProfileAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileStandard.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileWithSub.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileBase.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/LowScoreSegProfile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/OutputFile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/UserParameters.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Utility.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/InvalidCombination.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/DebugLog.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/ClustalWResources.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/VectorOutOfRange.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/SymMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Stats.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Help.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Alignment.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/AlignmentOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/ObjectiveScore.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Sequence.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Clustal.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './main.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled autoreconf: Leaving directory '.' + CFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables ' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables ' + export FCFLAGS + LDFLAGS=' -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags' + export LDFLAGS + CONFIGURE_TOP=. + '[' 1 = 1 ']' ++ find . -name config.guess -o -name config.sub + for i in $(find ${CONFIGURE_TOP} -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/mageia/config.sub ']' ++ basename ./config.sub + cp -af /usr/lib/rpm/mageia/config.sub ./config.sub + for i in $(find ${CONFIGURE_TOP} -name config.guess -o -name config.sub) ++ basename ./config.guess + '[' -f /usr/lib/rpm/mageia/config.guess ']' ++ basename ./config.guess + cp -af /usr/lib/rpm/mageia/config.guess ./config.guess + /usr/lib/rpm/mageia/force-as-needed-for-shared-lib-in-libtool Forcing -Wl,--as-needed in configure/libtool to workaround libtool bug (cf http://lists.gnu.org/archive/html/libtool-patches/2004-06/msg00002.html) + /usr/lib/rpm/mageia/drop-ld-no-undefined-for-shared-lib-modules-in-libtool + /usr/lib/rpm/mageia/fix-libtool-ltmain-from-overlinking + /usr/lib/rpm/mageia/fix-libtool-from-moving-options-after-libs . + /usr/lib/rpm/mageia/fix-dlsearch-path-in-libtool-for-multilib . lib64 + ./configure --host=aarch64-mageia-linux-gnu --build=aarch64-mageia-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info checking build system type... aarch64-mageia-linux-gnu checking host system type... aarch64-mageia-linux-gnu checking target system type... aarch64-mageia-linux-gnu building for linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make sets $(MAKE)... (cached) yes checking for aarch64-mageia-linux-gnu-gcc... no checking for gcc... gcc 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for aarch64-mageia-linux-gnu-g++... no checking for aarch64-mageia-linux-gnu-c++... no checking for aarch64-mageia-linux-gnu-gpp... no checking for aarch64-mageia-linux-gnu-aCC... no checking for aarch64-mageia-linux-gnu-CC... no checking for aarch64-mageia-linux-gnu-cxx... no checking for aarch64-mageia-linux-gnu-cc++... no checking for aarch64-mageia-linux-gnu-cl.exe... no checking for aarch64-mageia-linux-gnu-FCC... no checking for aarch64-mageia-linux-gnu-KCC... no checking for aarch64-mageia-linux-gnu-RCC... no checking for aarch64-mageia-linux-gnu-xlC_r... no checking for aarch64-mageia-linux-gnu-xlC... no checking for aarch64-mageia-linux-gnu-clang++... no checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for aarch64-mageia-linux-gnu-ranlib... no checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for _Bool... no checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for GNU libc compatible malloc... yes checking that generated files are newer than configure... done 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 + /usr/bin/make -O -j8 V=1 VERBOSE=1 Making all in m4 make[1]: Nothing to be done for 'all'. Making all in src /usr/bin/make all-recursive make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp 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] 96 | 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] 97 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)': ./fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 155 | auto_ptr fileParser; // Means we dont need to delete it! | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./fileInput/FileReader.cpp: At global scope: ./fileInput/FileReader.cpp:426:42: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 426 | void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp ./fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()': ./fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 37 | register int i; | ^ ./fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 38 | register char c; | ^ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 17 | auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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::string&)': ./tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 21 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 27 | auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/Tree.cpp:10: ./tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 280 | auto_ptr progAlignSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp ./tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)': ./tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 164 | register int i; | ^ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp 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] 96 | 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] 97 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:23: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp:31:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp:103:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 103 | auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp:195:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 195 | auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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::string*, bool*)': ./tree/TreeInterface.cpp:200:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 200 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:208:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 208 | auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::string*, std::vector*, int, int, bool*)': ./tree/TreeInterface.cpp:214:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 214 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:439:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 439 | auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::string*, std::vector*, int, int, bool*)': ./tree/TreeInterface.cpp:445:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 445 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:485:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 485 | auto_ptr | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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::string*, bool*)': ./tree/TreeInterface.cpp:490:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 490 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:503:1: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 503 | auto_ptr TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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::string*, bool*)': ./tree/TreeInterface.cpp:506:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 506 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp 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] 96 | 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] 97 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()': ./interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1190 | system(lin1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 231 | tmpnam (buffer); | ~~~~~~~^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp In file included from ./general/OutputFile.cpp:9: ./general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./general/OutputFile.h:8, from ./general/OutputFile.cpp:9: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp ./general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)': ./general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 475 | register int i; | ^ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp ./general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)': ./general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 53 | register int p; | ^ ./general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)': ./general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ ./general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)': ./general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp 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] 96 | 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] 97 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./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++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./main.cpp:16: ./fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp 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] 96 | 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] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()': ./alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 47 | register int sl; /* which have code = gap_pos2 */ | ^~ ./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()': ./alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 122 | register int sl; /* which have code = gap_pos2 */ | ^~ ./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()': ./alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 617 | register int sl; | ^~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp 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] 96 | 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] 97 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::align(std::string*, bool)': ./Clustal.cpp:162:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 162 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::string*)': ./Clustal.cpp:837:5: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 837 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -DHAVE_CONFIG_H -I. -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp 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] 96 | 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] 97 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./alignment/AlignmentOutput.cpp:512:40: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 512 | bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ ./alignment/AlignmentOutput.cpp:535:40: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 535 | string AlignmentOutput::openOutputFile(auto_ptr& outFile, string prompt, | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' g++ -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags -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 /usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': /home/iurt/rpmbuild/BUILD/clustalw-2.1/src/./multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[1]: Nothing to be done for 'all-am'. + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.QZI29K + umask 022 + cd /home/iurt/rpmbuild/BUILD + '[' 1 -eq 1 ']' + '[' /home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64 '!=' / ']' + rm -rf /home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64 ++ dirname /home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64 + mkdir -p /home/iurt/rpmbuild/BUILDROOT + mkdir /home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64 + cd clustalw-2.1 + '[' 1 -eq 1 ']' + /usr/bin/make install DESTDIR=/home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64 'INSTALL=/usr/bin/install -p' Making install in m4 make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/m4' make[2]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/m4' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/m4' make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/m4' Making install in src make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[2]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[3]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' /usr/bin/mkdir -p '/home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64/usr/bin' /usr/bin/install -p clustalw2 '/home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[2]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1/src' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1' make[2]: Entering directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1' make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/clustalw-2.1' + /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 2.1-10.mga9 --unique-debug-suffix -2.1-10.mga9.aarch64 --unique-debug-src-base clustalw-2.1-10.mga9.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /home/iurt/rpmbuild/BUILD/clustalw-2.1 extracting debug info from /home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64/usr/bin/clustalw2 dwz: ./usr/bin/clustalw2-2.1-10.mga9.aarch64.debug: Unknown debugging section .debug_line_str original debug info size: 11948kB, size after compression: 11948kB /usr/bin/sepdebugcrcfix: Updated 0 CRC32s, 1 CRC32s did match. 2058 blocks + /usr/lib/rpm/check-buildroot + '[' -n '' ']' + /usr/share/spec-helper/clean_files + '[' -n '' ']' + /usr/share/spec-helper/compress_files .xz + '[' -n '' ']' + /usr/share/spec-helper/relink_symlinks + '[' -n '' ']' + /usr/share/spec-helper/clean_perl + '[' -n '' ']' + /usr/share/spec-helper/lib_symlinks + '[' -n '' ']' + /usr/share/spec-helper/gprintify + '[' -n '' ']' + /usr/share/spec-helper/fix_mo + '[' -n '' ']' + /usr/share/spec-helper/fix_pamd + '[' -n '' ']' + /usr/share/spec-helper/remove_info_dir + '[' -n '' ']' + /usr/share/spec-helper/fix_eol + '[' -n '' ']' + /usr/share/spec-helper/check_desktop_files + '[' -n '' ']' + /usr/share/spec-helper/check_elf_files + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python3 1 0 + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-mangle-shebangs Processing files: clustalw-2.1-10.mga9.aarch64 Provides: clustalw = 2.1-10.mga9 clustalw(aarch-64) = 2.1-10.mga9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) Processing files: clustalw-debugsource-2.1-10.mga9.aarch64 Provides: clustalw-debugsource = 2.1-10.mga9 clustalw-debugsource(aarch-64) = 2.1-10.mga9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: clustalw-debuginfo-2.1-10.mga9.aarch64 Provides: clustalw-debuginfo = 2.1-10.mga9 clustalw-debuginfo(aarch-64) = 2.1-10.mga9 debuginfo(build-id) = 5126e9f895f0fcbb0ec2e2e2c789142bccb12316 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: clustalw-debugsource(aarch-64) = 2.1-10.mga9 Checking for unpackaged file(s): /usr/lib/rpm/check-files /home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64 Wrote: /home/iurt/rpmbuild/RPMS/aarch64/clustalw-2.1-10.mga9.aarch64.rpm Wrote: /home/iurt/rpmbuild/RPMS/aarch64/clustalw-debugsource-2.1-10.mga9.aarch64.rpm Wrote: /home/iurt/rpmbuild/RPMS/aarch64/clustalw-debuginfo-2.1-10.mga9.aarch64.rpm Executing(%clean): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.80kAoK + umask 022 + cd /home/iurt/rpmbuild/BUILD + cd clustalw-2.1 + /usr/bin/rm -rf /home/iurt/rpmbuild/BUILDROOT/clustalw-2.1-10.mga9.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(--clean): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.BcdKn2 + umask 022 + cd /home/iurt/rpmbuild/BUILD + rm -rf clustalw-2.1 + RPM_EC=0 ++ jobs -p + exit 0 D: [iurt_root_command] Success!