[Debian-med-packaging] Bug#1105296: consensuscore: FTBFS with make --shuffle=reverse: Fatal error: can't create /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o: No such file or directory

[Lucas Nussbaum]

Source: consensuscore
Version: 1.1.1+dfsg-8
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-shuffle

Hi,

GNU Make now has a --shuffle option that simulates non-deterministic ordering
of target prerequisites. See
https://trofi.github.io/posts/238-new-make-shuffle-mode.html and also previous
work in Debian by Santiago Vila:
https://people.debian.org/~sanvila/make-shuffle/

This package fails to build with make --shuffle=reverse.
This is likely to be caused by a missing dependency in
debian/rules or an upstream Makefile.

More information about this mass bug filing is available at
https://wiki.debian.org/qa.debian.org/FTBFS/Shuffle

Relevant part (hopefully):
> make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Logging/Logging.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Align/AffineAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Align/PairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Align/LinearAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Checksum.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Edna/EdnaCounts.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o
> make/Cpp.mk:24: update target '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o' due to: target does not exist
> g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now  -c src/C++/Statistics/Binomial.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o
> Assembler messages:
> Fatal error: can't create /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o: No such file or directory
> make[2]: *** [make/Cpp.mk:24: /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o] Error 1 shuffle=reverse


The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/reverse/consensuscore_1.1.1+dfsg-8_unstable_reverse.log

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects