Your message dated Sun, 03 Dec 2023 14:50:27 +0000
with message-id <[email protected]>
and subject line Bug#1015668: fixed in spades 3.15.5+dfsg-6
has caused the Debian Bug report #1015668,
regarding spades: ftbfs with LTO (link time optimization) enabled
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1015668: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1015668
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:spades
Version: 3.15.4+dfsg-2
Severity: minor
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-lto
This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled. For a background
for LTO please see
https://wiki.debian.org/ToolChain/LTO
The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures. The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.
To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:
export DEB_BUILD_MAINT_OPTIONS = optimize=+lto
Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:
export DEB_BUILD_MAINT_OPTIONS = optimize=-lto
or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/spades_3.15.4+dfsg-2_unstable_dpkglto.log
The last lines of the build log are at the end of this report.
[...]
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects
-Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o"
"../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o
../../bin/spades-kmercount ../../common/libcommon_modules.a
../../common/utils/libversion.a ../../ext/cppformat/libformat.a
../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a
../../common/pipeline/libpipeline.a ../../common/io/libinput.a
../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a
../../common/modules/path_extend/libpath_extend.a -lssw
../../common/io/binary/libbinary_io.a
../../common/modules/coverage_model/libcoverage_model.a -lnlopt
../../ext/gqf/libgqf.a ../../common/modules/libmodules.a
../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a
../../common/utils/lib
version.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a
/usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt
-ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so
/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so
/usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a
../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so
[ 91%] Linking CXX executable ../../bin/spades-read-filter
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake
-E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects
-Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o"
"../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o
../../bin/spades-read-filter ../../common/libcommon_modules.a
../../common/utils/libversion.a ../../ext/cppformat/libformat.a
../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a
../../common/pipeline/libpipeline.a ../../common/io/libinput.a
../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a
../../common/modules/path_extend/libpath_extend.a -lssw
../../common/io/binary/libbinary_io.a
../../common/modules/coverage_model/libcoverage_model.a -lnlopt
../../ext/gqf/libgqf.a ../../common/modules/libmodules.a
../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a
../../commo
n/utils/libversion.a ../../ext/cppformat/libformat.a
../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so
/usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm
/usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so
/usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a
../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa
/usr/lib/x86_64-linux-gnu/libz.so
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp: In member
function 'size_t KMerClustering::SubClusterSingle(const std::vector<long
unsigned int>&, std::vector<std::vector<long unsigned int> >&)':
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning:
this 'for' clause does not guard... [-Wmisleading-indentation]
357 | for (uint32_t j=0; j<K; ++j) std::cout << std::setw(3) <<
(unsigned)getQual(kms, j) << " "; std::cout << "\n";
| ^~~
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:357:101: note:
...this statement, but the latter is misleadingly indented as if it were
guarded by the 'for'
357 | for (uint32_t j=0; j<K; ++j) std::cout << std::setw(3) <<
(unsigned)getQual(kms, j) << " "; std::cout << "\n";
|
^~~
[ 91%] Building CXX object
projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /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/hammer
-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 -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion
-Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT
projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF
CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o
CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_data.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-kmer-estimating
[ 91%] Building CXX object
projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /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/hammer
-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 -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion
-Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT
projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF
CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o
CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c
/<<PKGBUILDDIR>>/assembler/src/proj
ects/hammer/config_struct_hammer.cpp
[ 91%] Building CXX object
projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /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/hammer
-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 -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion
-Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT
projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF
CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o
CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/read_c
orrector.cpp
[ 91%] Linking CXX executable ../../bin/spades-core
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E
cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects
-Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o"
"CMakeFiles/spades-core.dir/main.cpp.o"
"CMakeFiles/spades-core.dir/series_analysis.cpp.o"
"CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o"
"../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o
../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a
../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a
../../common/utils/libversion.a ../../ext/cppformat/libformat.a
../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a
../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a
../../common/pipeline/libpipeline.a ../../common/io/libinput.a
../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a
../../common/modul
es/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a
../../common/modules/coverage_model/libcoverage_model.a -lnlopt
../../ext/gqf/libgqf.a ../../common/modules/libmodules.a
../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a
../../common/utils/libversion.a ../../ext/cppformat/libformat.a
../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so
/usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread
/usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so
/usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a
../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa
/usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a
../../ext/easel/libeasel.a -lm
[ 91%] Building CXX object
projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o
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 -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion
-Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT
projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF
CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o
CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c
/<<PKGBUILDDIR>>/assemb
ler/src/projects/corrector/config_struct.cpp
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/read_corrector.cpp: In member
function 'std::string ReadCorrector::CorrectReadRight(const string&, const
string&, size_t)':
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/read_corrector.cpp:72:57:
warning: conversion from 'long unsigned int' to 'double' may change value
[-Wconversion]
72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) +
1;
| ~~~~~~~~~~^~~~~~~~~~~
[ 91%] Building CXX object
projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o
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 -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion
-Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT
projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF
CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o
CMakeFiles/spades-corrector-core.dir/main.cpp.o -c
/<<PKGBUILDDIR>>/assembler/src/projects/corrector/
main.cpp
In file included from
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/globals.hpp:11,
from
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/hammer_tools.hpp:19,
from
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:11:
In member function 'NibbleString<21u, 6u, unsigned long>::set(unsigned long,
unsigned char)',
inlined from 'NibbleString<21u, 6u, unsigned long>::NibbleString(unsigned
char const*)' at
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_stat.hpp:62:16,
inlined from 'KMerStat::KMerStat(unsigned int, float, unsigned char
const*)' at /<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_stat.hpp:121:96,
inlined from 'KMerClustering::SubClusterSingle(std::vector<unsigned long,
std::allocator<unsigned long> > const&, std::vector<std::vector<unsigned long,
std::allocator<unsigned long> >, std::allocator<std::vector<unsigned long,
std::allocator<unsigned long> > > >&)' at
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:433:81:
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_stat.hpp:69:40: warning:
'MEM <const long unsigned int[2]> [(value_type &)&kms + 8][0]' may be used
uninitialized [-Wmaybe-uninitialized]
69 | storage_[idx] = (storage_[idx] & ~(MaxValue << offset)) |
((value & MaxValue) << offset);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp: In member
function 'KMerClustering::SubClusterSingle(std::vector<unsigned long,
std::allocator<unsigned long> > const&, std::vector<std::vector<unsigned long,
std::allocator<unsigned long> >, std::allocator<std::vector<unsigned long,
std::allocator<unsigned long> > > >&)':
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:433:22: note:
'kms' declared here
433 | KMerStat kms(0 /* cnt */, 1.0 /* total quality */, NULL
/*quality */);
| ^~~
[ 91%] Building CXX object
projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /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/hammer
-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 -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion
-Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT
projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF
CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o
CMakeFiles/spades-hammer.dir/expander.cpp.o -c
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/expander.cpp
[ 91%] Linking CXX executable ../../bin/spades-corrector-core
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake
-E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects
-Wl,-z,relro -Wl,-z,now
"CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o"
"CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o"
"CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o"
"CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o"
"CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o"
"CMakeFiles/spades-corrector-core.dir/main.cpp.o"
"../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o
../../bin/spades-corrector-core ../../common/io/libinput.a
../../common/libcommon_modules.a ../../common/utils/libversion.a
../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a
../../common/stages/libstages.a ../../common/pipeline/libpipeline.a
../../common/io/libinput.a ../../ext/samtools/libsamtools.a
../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a
../../common/modules/path_extend/libpath_extend.a -lssw
../../common/modules/coverage_model/libcoverage_model.a -lnlopt
../../ext/gqf/libgqf.a ../../common/modules/libmodules.a
../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a
../../common/utils/libversion.a ../../ext/cppformat/libformat.a
../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so
/usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm
/usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so
/usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a
../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa
/usr/lib/x86_64-linux-gnu/libz.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-kmercount
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-read-filter
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-corrector-core
[ 93%] Linking CXX executable ../../bin/spades-hammer
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E
cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects
-Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o"
"CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o"
"CMakeFiles/spades-hammer.dir/hamcluster.cpp.o"
"CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o"
"CMakeFiles/spades-hammer.dir/kmer_data.cpp.o"
"CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o"
"CMakeFiles/spades-hammer.dir/read_corrector.cpp.o"
"CMakeFiles/spades-hammer.dir/expander.cpp.o"
"../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o
../../bin/spades-hammer ../../common/libcommon_modules.a
../../common/io/libinput.a ../../common/utils/libutils.a
../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a
../../common/utils/libversion.a ../../ext/cppformat/libformat.a
../../common/paired_info/libpaired_info.a ../../common/stages
/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a
../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a
../../common/modules/path_extend/libpath_extend.a -lssw
../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a
../../common/modules/coverage_model/libcoverage_model.a -lnlopt
../../common/modules/libmodules.a
../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a
../../common/utils/libversion.a ../../ext/cppformat/libformat.a
../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so
/usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm
/usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so
/usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a
../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa
/usr/lib/x86_64-linux-gnu/libz.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 93%] Built target spades-hammer
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 93%] Built target spades-core
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: spades
Source-Version: 3.15.5+dfsg-6
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
spades, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated spades package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 03 Dec 2023 14:52:02 +0100
Source: spades
Architecture: source
Version: 3.15.5+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1015668
Changes:
spades (3.15.5+dfsg-6) unstable; urgency=medium
.
* d/rules: disable lto builds.
Upstream is aware that there is a problem with lto appllied on spades,
and this seems to be caused by a lingering compiler bug. (Closes: #1015668)
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