* Package: sci-biology/clustal-omega-1.2.4-r1:0 * 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 clustal-omega-1.2.4.tar.gz to /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4 ... * Running eautoreconf in '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4' ... * Running 'libtoolize --install --copy --force --automake' ... [ ok ] * Running 'aclocal -I m4 --system-acdir=/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/temp/aclocal' ... [ ok ] * Running 'autoconf --force' ... [ ok ] * Running 'autoheader' ... [ ok ] * Running 'automake --add-missing --copy --force-missing' ... [ ok ] * Running elibtoolize in: clustal-omega-1.2.4/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.4.3 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4 ... * econf: updating clustal-omega-1.2.4/config.guess with /usr/share/gnuconfig/config.guess * econf: updating clustal-omega-1.2.4/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 --disable-silent-rules --disable-static --docdir=/usr/share/doc/clustal-omega-1.2.4-r1 --htmldir=/usr/share/doc/clustal-omega-1.2.4-r1/html --with-sysroot=/ --libdir=/usr/lib64 configure: Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 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 race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports the include directive... yes (GNU style) checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-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 x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none 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 wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-file... no checking for file... file checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... x86_64-pc-linux-gnu-dlltool checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... / checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc checking whether the compiler supports GNU C... (cached) yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... (cached) none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether the compiler supports GNU C++... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for x86_64-pc-linux-gnu-g++ option to enable C++11 features... none needed checking dependency style of x86_64-pc-linux-gnu-g++... none checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for egrep... (cached) /bin/grep -E checking for assert.h... yes checking for ctype.h... yes checking for float.h... yes checking for limits.h... yes checking for math.h... yes checking for memory.h... yes checking for stdarg.h... yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 16 checking if malloc debugging is wanted... no checking whether to build with debug information... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4 ... make -j4 Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src' make all-recursive make[2]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src' Making all in hhalign make[3]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src/hhalign' /bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -c -o hhalign.lo hhalign.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o In file included from hhalign.cpp:70: hhhmm-C.h: In member function 'void HMM::UseSecStrucDependentGapPenalties()': hhhmm-C.h:1748:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1748 | iis[0]=iis[L]=0; | ~~~~~~^~ hhhmm-C.h:1734:17: note: at offset [-2147483648, -1] into destination object 'iis' of size [0, 2147483647] 1734 | unsigned char iis[par.maxResLen]; // inside-integer array | ^~~ during GIMPLE pass: ch_vect In file included from hhalign.cpp:75: hhhitlist-C.h: In member function 'void HitList::SVD(double**, int, double*, double**)': hhhitlist-C.h:2919:1: internal compiler error: in check_loop_closed_ssa_def, at tree-ssa-loop-manip.cc:647 2919 | HitList::SVD(double **A, int n, double w[], double **V) | ^~~~~~~ 0x5633810ca20d internal_error(char const*, ...) ???:0 0x56337f081c60 fancy_abort(char const*, int, char const*) ???:0 0x56337fd540a6 verify_loop_closed_ssa(bool, loop*) ???:0 Please submit a full bug report, with preprocessed source (by using -freport-bug). Please include the complete backtrace with any bug report. See for instructions. make[3]: *** [Makefile:457: hhalign.lo] Error 1 make[3]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src/hhalign' make[2]: *** [Makefile:663: all-recursive] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src' make[1]: *** [Makefile:431: all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src' make: *** [Makefile:482: all-recursive] Error 1 * ERROR: sci-biology/clustal-omega-1.2.4-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/clustal-omega-1.2.4-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/clustal-omega-1.2.4-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:clustal-omega-1.2.4-r1:20231204-110826.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4' * S: '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4'