Control: tags -1 + confirmed Control: forwarded -1 https://github.com/ablab/spades/issues/1007
Hi all,
I gave another go at this issue today, and the relevant part of
the build log seemed to be:
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/corrector &&
/usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1
-I/<<PKGBUILDDIR>>/assembler/src/include
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include
-I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common
-I/<<PKGBUILDDIR>>/assembler/src/projects/corrector
-I/<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/include -isystem
/<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem
/<<PKGBUILDDIR>>/assembler/ext/include -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion
-Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT
projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o
-MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o
CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c
/<<PKGBUILDDIR>>/assembler/src/projects/corrector/dataset_processor.cpp
lto1: fatal error: multiple prevailing defs for 'insert'
compilation terminated.
lto-wrapper: fatal error: /usr/bin/c++ returned 1 exit status
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
make[4]: ***
[projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make:131:
bin/spades-truseq-scfcorrection] Error 1
Feeding 'gcc lto "fatal error: multiple prevailing defs for"' to
a search engine shown multiple results suggesting probable
compiler bugs, notably as mentioned in upstream bug report[1],
which itself redirects to bug Gcc#86490[2]. I'm considering an
upload of spades which ensures lto builds are always disabled.
[1]: https://github.com/ablab/spades/issues/1007
[2]: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86490
Have a nice Sunday, :)
--
.''`. Étienne Mollier <[email protected]>
: :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/5, please excuse my verbosity
`- on air: 7for4 - Rushian
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