[Debian-med-packaging] Bug#1015668: spades: ftbfs with LTO: supplemental

[Étienne Mollier]

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 <emollier at debian.org>
 : :' :  gpg: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/5, please excuse my verbosity
   `-    on air: 7for4 - Rushian
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20231203/3d57ac81/attachment.sig>