sci-biology:clustalw-2.1-r2:20230903-191927.log

sci-biology:clustalw-2.1-r2:20230903-191927.log (text/plain), 9.50 KB, created by Toralf Förster on 2023-09-03 19:48:28 UTC

 * Package:    sci-biology/clustalw-2.1-r2:2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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<short>& 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<short>& 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<short>& 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<short>& 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<short>& 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<short>& 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>& fileParser);
                                     ^
./fileInput/FileReader.cpp:155:5: error: no template named 'auto_ptr'
    auto_ptr<FileParser> 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>& 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'