* Package: sci-biology/yass-1.14-r3:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 dmalloc elibc_glibc kernel_linux lowmem * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking yass-1.14.tar.gz to /var/tmp/portage/sci-biology/yass-1.14-r3/work >>> Source unpacked in /var/tmp/portage/sci-biology/yass-1.14-r3/work >>> Preparing source in /var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14 ... * Applying 1.14-as-needed.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14' ... * Running 'aclocal --system-acdir=/var/tmp/portage/sci-biology/yass-1.14-r3/temp/aclocal' ... [ ok ] * Running 'autoconf --force' ... [ ok ] * Running 'automake --add-missing --copy --force-missing' ... [ ok ] * Running elibtoolize in: yass-1.14/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14 ... * econf: updating yass-1.14/build/config.guess with /usr/share/gnuconfig/config.guess * econf: updating yass-1.14/build/config.sub with /usr/share/gnuconfig/config.sub * econf: updating yass-1.14/config.guess with /usr/share/gnuconfig/config.guess * econf: updating yass-1.14/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 --docdir=/usr/share/doc/yass-1.14-r3 --htmldir=/usr/share/doc/yass-1.14-r3/html --libdir=/usr/lib64 --disable-threads --enable-lowmemory --with-dmalloc 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 checking whether make sets $(MAKE)... yes 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 for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c 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 sys/time.h... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for assert.h... yes checking for math.h... yes checking for errno.h... yes checking for inline... inline checking for error_at_line... yes checking for GNU libc compatible malloc... yes checking for working strtod... yes checking for floor... no checking for memset... yes checking for clock... yes checking for pow... no checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strtol... yes checking for strtoul... yes detected memory parameter: low memory checking if malloc debugging is wanted... yes checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14 ... make -j4 Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14/src' x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"yass\" -DPACKAGE_TARNAME=\"yass\" -DPACKAGE_VERSION=\"1.14\" -DPACKAGE_STRING=\"yass\ 1.14\" -DPACKAGE_BUGREPORT=\"laurent.noe@lifl.fr\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_ASSERT_H=1 -DHAVE_MATH_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MALLOC=1 -DHAVE_MEMSET=1 -DHAVE_CLOCK=1 -DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_STRTOL=1 -DHAVE_STRTOUL=1 -DWITH_DMALLOC=1 -DPACKAGE=\"yass\" -DVERSION=\"1.14\" -I. -O3 -pipe -march=native -fno-diagnostics-color -DLOW_MEMORY -c -o align.o align.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"yass\" -DPACKAGE_TARNAME=\"yass\" -DPACKAGE_VERSION=\"1.14\" -DPACKAGE_STRING=\"yass\ 1.14\" -DPACKAGE_BUGREPORT=\"laurent.noe@lifl.fr\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_ASSERT_H=1 -DHAVE_MATH_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MALLOC=1 -DHAVE_MEMSET=1 -DHAVE_CLOCK=1 -DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_STRTOL=1 -DHAVE_STRTOUL=1 -DWITH_DMALLOC=1 -DPACKAGE=\"yass\" -DVERSION=\"1.14\" -I. -O3 -pipe -march=native -fno-diagnostics-color -DLOW_MEMORY -c -o assemble.o assemble.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"yass\" -DPACKAGE_TARNAME=\"yass\" -DPACKAGE_VERSION=\"1.14\" -DPACKAGE_STRING=\"yass\ 1.14\" -DPACKAGE_BUGREPORT=\"laurent.noe@lifl.fr\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_ASSERT_H=1 -DHAVE_MATH_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MALLOC=1 -DHAVE_MEMSET=1 -DHAVE_CLOCK=1 -DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_STRTOL=1 -DHAVE_STRTOUL=1 -DWITH_DMALLOC=1 -DPACKAGE=\"yass\" -DVERSION=\"1.14\" -I. -O3 -pipe -march=native -fno-diagnostics-color -DLOW_MEMORY -c -o avl.o avl.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"yass\" -DPACKAGE_TARNAME=\"yass\" -DPACKAGE_VERSION=\"1.14\" -DPACKAGE_STRING=\"yass\ 1.14\" -DPACKAGE_BUGREPORT=\"laurent.noe@lifl.fr\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_ASSERT_H=1 -DHAVE_MATH_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MALLOC=1 -DHAVE_MEMSET=1 -DHAVE_CLOCK=1 -DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_STRTOL=1 -DHAVE_STRTOUL=1 -DWITH_DMALLOC=1 -DPACKAGE=\"yass\" -DVERSION=\"1.14\" -I. -O3 -pipe -march=native -fno-diagnostics-color -DLOW_MEMORY -c -o display.o display.c assemble.c: In function ‘Assemble_Single’: assemble.c:116:94: error: implicit declaration of function ‘hashVerifie’ [-Wimplicit-function-declaration] 116 | ) putHashOneDiagValue (&table,index,(long int)value);hashVerifie(&table,"here",index); | ^~~~~~~~~~~ assemble.c:305:19: note: in expansion of macro ‘PUT_TAB’ 305 | PUT_TAB(last_tuple_ptr_with_diag,observed_diagonal,t); | ^~~~~~~ make[1]: *** [Makefile:399: assemble.o] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory '/var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14/src' make: *** [Makefile:358: all-recursive] Error 1 * ERROR: sci-biology/yass-1.14-r3::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/yass-1.14-r3::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/yass-1.14-r3::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:yass-1.14-r3:20231204-101733.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/yass-1.14-r3/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/yass-1.14-r3/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14' * S: '/var/tmp/portage/sci-biology/yass-1.14-r3/work/yass-1.14'