[Debian-med-packaging] Bug#1097913: spades: ftbfs with GCC-15
Matthias Klose
doko at debian.org
Mon Feb 17 17:54:26 GMT 2025
Package: src:spades
Version: 3.15.5+dfsg-8
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-15
[This bug is NOT targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/spades_3.15.5+dfsg-8_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other Common build failures are new warnings resulting in build failures
with -Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-15/porting_to.html
[...]
/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined
5 | safe_mutex_lock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~
[ 40%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regerror.c
[ 41%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c
[ 41%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c
In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8:
/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined
8 | safe_mutex_unlock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~~~
/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined
5 | safe_mutex_lock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7:
/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined
240 | unpackInt16(const uint8_t* buffer);
| ^~~~~~~~~~~
[ 41%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c
[ 43%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -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 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp
In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11,
from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10:
/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined
8 | safe_mutex_unlock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~~~
/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined
5 | safe_mutex_lock(pthread_mutex_t *mutex);
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7:
/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined
240 | unpackInt16(const uint8_t* buffer);
| ^~~~~~~~~~~
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -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 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp
[ 43%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regfree.c
[ 43%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -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 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp
[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -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 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp
[ 44%] Linking CXX static library libBamTools.a
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1
/usr/bin/ar qc libBamTools.a CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
/usr/bin/ranlib libBamTools.a
make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu'
[ 44%] Built target BamTools
[ 44%] Linking CXX static library libllvm-support.a
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake
cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1
/usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o"
/usr/bin/ranlib libllvm-support.a
make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu'
[ 44%] Built target llvm-support
make[3]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:29: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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