* Package: sci-biology/dialign-tx-1.0.2-r2:0 * 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 DIALIGN-TX_1.0.2.tar.gz to /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2 ... * Applying dialign-tx-1.0.2-fix-build-system.patch ... [ ok ] * Applying dialign-tx-1.0.2-implicits.patch ... [ ok ] * Applying dialign-tx-1.0.2-modernize.patch ... [ ok ] * Applying dialign-tx-1.0.2-gnu89-inline.patch ... [ ok ] * Applying dialign-tx-1.0.2-fno-common.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2 ... make -O -j4 -C source clean make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' rm -rf *.o *rtl *jump *addre* *cfg *life *reg *reload *flow* *stack museq dialign-tx make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make -O -j4 -C source make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o parameters.o parameters.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o museq.o museq.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o diag.o diag.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o io.o io.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o alig.o alig.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o assemble.o assemble.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o prob.o prob.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o translate.o translate.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -c -o orf.o orf.c make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' rm -f ./museq x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -o ./museq \ ./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o \ -pipe -Wall -lm museq.c:58:13: error: type of ‘simple_aligner’ does not match original declaration [-Werror=lto-type-mismatch] 58 | extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol, | ^ assemble.c:398:6: note: return value type mismatch 398 | char simple_aligner(struct seq_col *scol, struct diag_col *dcol, | ^ assemble.c:398:6: note: type ‘char’ should match type ‘int’ assemble.c:398:6: note: ‘simple_aligner’ was previously declared here lto1: some warnings being treated as errors lto-wrapper: fatal error: x86_64-pc-linux-gnu-gcc returned 1 exit status compilation terminated. /usr/lib/gcc/x86_64-pc-linux-gnu/15/../../../../x86_64-pc-linux-gnu/bin/ld: error: lto-wrapper failed collect2: error: ld returned 1 exit status make: *** [Makefile:34: museq] Error 1 make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source' * ERROR: sci-biology/dialign-tx-1.0.2-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/dialign-tx-1.0.2-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/dialign-tx-1.0.2-r2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:dialign-tx-1.0.2-r2:20241006-221256.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2' * S: '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2'