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Gentoo's Bugzilla – Attachment 905040 Details for
Bug 941102
sci-biology/dialign-tx-1.0.2-r2 - [libtool] [gcc-15] museq.c: error: type of simple_aligner does not match original declaration [-Werror=lto-type-mismatch]
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sci-biology:dialign-tx-1.0.2-r2:20241006-221256.log
sci-biology:dialign-tx-1.0.2-r2:20241006-221256.log (text/plain), 6.80 KB, created by
Toralf Förster
on 2024-10-07 08:40:01 UTC
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Description:
sci-biology:dialign-tx-1.0.2-r2:20241006-221256.log
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Creator:
Toralf Förster
Created:
2024-10-07 08:40:01 UTC
Size:
6.80 KB
patch
obsolete
> * 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 âsimple_alignerâ 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 âcharâ should match type âintâ >assemble.c:398:6: note: âsimple_alignerâ 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' >
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