* Package: sci-biology/clustalw-2.1-r2:2 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking clustalw-2.1.tar.gz to /var/tmp/portage/sci-biology/clustalw-2.1-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/clustalw-2.1-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1 ... * econf: updating clustalw-2.1/config.guess with /usr/share/gnuconfig/config.guess * econf: updating clustalw-2.1/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --disable-dependency-tracking --docdir=/usr/share/doc/clustalw-2.1-r2 --htmldir=/usr/share/doc/clustalw-2.1-r2/html --libdir=/usr/lib64 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu building for linux-gnu checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make sets $(MAKE)... (cached) yes checking for x86_64-pc-linux-gnu-gcc... clang checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang accepts -g... yes checking for clang option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of clang... none checking whether we are using the GNU C++ compiler... yes checking whether clang++ accepts -g... yes checking dependency style of clang++... none checking for x86_64-pc-linux-gnu-ranlib... llvm-ranlib checking how to run the C++ preprocessor... clang++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1 ... make -j5 Making all in m4 make[1]: Entering directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/m4' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/m4' Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/src' make all-recursive make[2]: Entering directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/src' make[3]: Entering directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/src' clang++ -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp clang++ -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp clang++ -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp clang++ -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp clang++ -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp In file included from ./pairwise/FullPairwiseAlign.cpp:9: In file included from ./pairwise/FullPairwiseAlign.h:9: In file included from ./pairwise/PairwiseAlignBase.h:10: In file included from ./pairwise/../alignment/Alignment.h:42: In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printVectorToFile(vector& temp, char* name = "tempfi... ^ In file included from ./pairwise/FastPairwiseAlign.cpp:10: In file included from ./pairwise/FastPairwiseAlign.h:9: In file included from ./pairwise/PairwiseAlignBase.h:10: In file included from ./pairwise/../alignment/Alignment.h:42: In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printVectorToFile(vector& temp, char* name = "tempfi... ^ In file included from ./fileInput/FileReader.cpp:29: In file included from ./fileInput/FileReader.h:12: In file included from ./fileInput/../alignment/Alignment.h:42: In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printVectorToFile(vector& temp, char* name = "tempfi... ^ In file included from ./fileInput/FileReader.cpp:29: ./fileInput/FileReader.h:42:38: error: no template named 'auto_ptr' void checkInfile(int* nseqs, auto_ptr& fileParser); ^ ./fileInput/FileReader.cpp:155:5: error: no template named 'auto_ptr' auto_ptr fileParser; // Means we dont need to delete it! ^ ./fileInput/FileReader.cpp:426:42: error: no template named 'auto_ptr' void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) ^ 2 warnings and 3 errors generated. 2 warnings generated. make[3]: *** [Makefile:584: FileReader.o] Error 1 make[3]: *** Waiting for unfinished jobs.... 2 warnings generated. make[3]: Leaving directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/src' make[2]: *** [Makefile:1258: all-recursive] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/src' make[1]: *** [Makefile:371: all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1/src' make: *** [Makefile:264: all-recursive] Error 1 * ERROR: sci-biology/clustalw-2.1-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/clustalw-2.1-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/clustalw-2.1-r2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:clustalw-2.1-r2:20230903-191927.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustalw-2.1-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustalw-2.1-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1' * S: '/var/tmp/portage/sci-biology/clustalw-2.1-r2/work/clustalw-2.1'