[Debian-med-packaging] Bug#1133636: stacks: ftbfs with GCC-16
Emanuele Rocca
ema at debian.org
Mon Apr 13 14:11:17 BST 2026
Package: src:stacks
Version: 2.68+dfsg-2
Severity: important
Tags: sid forky ftbfs
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-16
Hi,
stacks fails to build in a test rebuild on at least amd64 and arm64 with
gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this
report will be raised before the forky release.
The full build log can be found at:
https://people.debian.org/~ema/gcc-16-rebuilds/output-1/stacks_arm64.build.xz
The last lines of the build log are at the end of this report.
To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures include unused (but set) variables, array subscripts
partly outside array bounds, and new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-16/porting_to.html
Please only close this issue after double-checking that the package can be
built correctly with GCC 16.
Please do not reassign this bug to another package. If a fix in another package
is required, then file a bug for the other package (or clone), and mark this
bug as blocked by the bug in the other package.
[...]
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/sstacks.o src/sstacks.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/process_radtags.o src/process_radtags.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/clean.o src/clean.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/file_io.o src/file_io.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/write.o src/write.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/process_shortreads.o src/process_shortreads.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/kmer_filter.o src/kmer_filter.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/clone_filter.o src/clone_filter.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/populations.o src/populations.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/bootstrap.o src/bootstrap.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/export_formats.o src/export_formats.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/mapping_utils.o src/mapping_utils.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/PopSum.o src/PopSum.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/Hwp.o src/Hwp.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/phasedstacks.o src/phasedstacks.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/tsv2bam.o src/tsv2bam.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/gstacks.o src/gstacks.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/debruijn.o src/debruijn.cc
g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/SuffixTree.o src/SuffixTree.cc
src/MetaPopInfo.cc: In member function ‘void MetaPopInfo::fill_pop_indexes(std::map<int, std::pair<int, int> >&) const’:
src/MetaPopInfo.cc:427:30: warning: narrowing conversion of ‘i’ from ‘std::size_t’ {aka ‘long unsigned int’} to ‘int’ [-Wnarrowing]
427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} );
| ^
src/models.cc: In member function ‘double MarukiLowModel::calc_ln_weighted_sum(double, double, double, const LikData&) const’:
src/models.cc:736:30: error: ‘numeric_limits’ is not a member of ‘std’
736 | if (weighted_sum >= std::numeric_limits<double>::min()) {
| ^~~~~~~~~~~~~~
src/models.cc:736:45: error: expected primary-expression before ‘double’
736 | if (weighted_sum >= std::numeric_limits<double>::min()) {
| ^~~~~~
src/models.cc:736:45: error: expected ‘)’ before ‘double’
736 | if (weighted_sum >= std::numeric_limits<double>::min()) {
| ~ ^~~~~~
| )
src/models.cc: In member function ‘virtual SiteCall MarukiLowModel::call(const SiteCounts&) const’:
src/models.cc:865:31: error: ‘numeric_limits’ is not a member of ‘std’
865 | double lnl_dimorph = std::numeric_limits<double>::lowest();
| ^~~~~~~~~~~~~~
src/models.cc:865:46: error: expected primary-expression before ‘double’
865 | double lnl_dimorph = std::numeric_limits<double>::lowest();
| ^~~~~~
In file included from /usr/include/c++/16/cassert:46,
from src/constants.h:39,
from src/models.h:24,
from src/models.cc:30:
src/models.cc:883:31: error: ‘numeric_limits’ is not a member of ‘std’
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^~~~~~~~~~~~~~
src/models.cc:883:46: error: expected primary-expression before ‘double’
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^~~~~~
src/models.cc:883:46: error: expected ‘)’ before ‘double’
src/models.cc:883:46: error: expected ‘)’ before ‘double’
src/models.cc:883:5: note: to match this ‘(’
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^~~~~~
src/models.cc: In member function ‘double MarukiLowModel::calc_ln_weighted_sum(double, double, double, const LikData&) const’:
src/models.cc:744:1: warning: control reaches end of non-void function [-Wreturn-type]
744 | }
| ^
make[3]: *** [Makefile:1121: src/models.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
make[2]: *** [Makefile:1138: all-recursive] Error 1
make[2]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
make[1]: *** [Makefile:778: all] Error 2
make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
dh_auto_build: error: make -j128 returned exit code 2
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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