Package: src:sambamba Version: 1.0.1+dfsg-2 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202510/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:sambamba, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean mkdir -p obj-x86_64-linux-gnu dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_clean rm -rf /<<PKGBUILDDIR>>/output/ rm -f test.log make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary mkdir -p obj-x86_64-linux-gnu dh binary --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_configure -- -Doptimize_strong=true -Dcpp_link_args="-wi -L=-z -L=relro /usr/lib/x86_64-linux-gnu/libhts.a -L=-lz -L=-lcrypto -L=-lcurl -L=-llzma -L=-lbz2 -L=-ldeflate -L=-llz4" cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1 -Doptimize_strong=true -Dcpp_link_args="-wi -L=-z -L=relro /usr/lib/x86_64-linux-gnu/libhts.a -L=-lz -L=-lcrypto -L=-lcurl -L=-llzma -L=-lbz2 -L=-ldeflate -L=-llz4" The Meson build system Version: 1.9.1 Source dir: /<<PKGBUILDDIR>> Build dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu Build type: native build Project name: Sambamba Project version: 1.0.1 C compiler for the host machine: cc (gcc 15.2.0 "cc (Debian 15.2.0-7) 15.2.0") C linker for the host machine: cc ld.bfd 2.45 D compiler for the host machine: ldc2 (llvm 1.41.0 "LDC - the LLVM D compiler (1.41.0):") D linker for the host machine: ldc2 ld.bfd 2.45 Host machine cpu family: x86_64 Host machine cpu: x86_64 ../meson.build:18: WARNING: Project does not target a minimum version but uses feature deprecated since '0.56.0': meson.source_root. use meson.project_source_root() or meson.global_source_root() instead. ../meson.build:19: WARNING: Project does not target a minimum version but uses feature deprecated since '0.56.0': meson.build_root. use meson.project_build_root() or meson.global_build_root() instead. Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency liblz4 found: YES 1.10.0 Run-time dependency zlib found: YES 1.3.1 Program ldc2 found: YES (/usr/bin/ldc2) Program mkdir found: YES (/usr/bin/mkdir) ../meson.build:220: WARNING: Project does not target a minimum version but uses feature deprecated since '0.55.0': ExternalProgram.path. use ExternalProgram.full_path() instead WARNING: You should add the boolean check kwarg to the run_command call. It currently defaults to false, but it will default to true in meson 2.0. See also: https://github.com/mesonbuild/meson/issues/9300 ../meson.build:227: WARNING: Project does not target a minimum version but uses feature deprecated since '0.55.0': ExternalProgram.path. use ExternalProgram.full_path() instead Program /<<PKGBUILDDIR>>/test/test_suite.sh found: YES (/<<PKGBUILDDIR>>/test/test_suite.sh) Build targets in project: 1 WARNING: Deprecated features used: * 0.55.0: {'ExternalProgram.path'} * 0.56.0: {'meson.build_root', 'meson.source_root'} Sambamba 1.0.1 User defined options buildtype : plain cpp_link_args : -wi -L=-z -L=relro /usr/lib/x86_64-linux-gnu/libhts.a -L=-lz -L=-lcrypto -L=-lcurl -L=-llzma -L=-lbz2 -L=-ldeflate -L=-llz4 libdir : lib/x86_64-linux-gnu localstatedir : /var optimize_strong : true prefix : /usr python.bytecompile: -1 sysconfdir : /etc wrap_mode : nodownload Found ninja-1.12.1 at /usr/bin/ninja make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j2 -v [1/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_main.d.o.deps -of=sambamba.p/sambamba_main.d.o -c ../sambamba/main.d [2/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d [3/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_flagstat.d.o.deps -of=sambamba.p/sambamba_flagstat.d.o -c ../sambamba/flagstat.d [4/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_depth.d.o.deps -of=sambamba.p/sambamba_depth.d.o -c ../sambamba/depth.d [5/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_index.d.o.deps -of=sambamba.p/sambamba_index.d.o -c ../sambamba/index.d [6/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_markdup2.d.o.deps -of=sambamba.p/sambamba_markdup2.d.o -c ../sambamba/markdup2.d [7/140] ldc2 -I=sambamba.p 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-I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_sort.d.o.deps -of=sambamba.p/sambamba_sort.d.o -c ../sambamba/sort.d [11/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_subsample.d.o.deps -of=sambamba.p/sambamba_subsample.d.o -c ../sambamba/subsample.d [12/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_pileup.d.o.deps -of=sambamba.p/sambamba_pileup.d.o -c ../sambamba/pileup.d [13/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_file.d.o.deps -of=sambamba.p/sambamba_utils_common_file.d.o -c ../sambamba/utils/common/file.d [14/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_bed.d.o.deps -of=sambamba.p/sambamba_utils_common_bed.d.o -c ../sambamba/utils/common/bed.d [15/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_intervaltree.d.o.deps 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-release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_virtualoffset.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_virtualoffset.d.o -c ../BioD/bio/core/bgzf/virtualoffset.d [35/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_call.d.o.deps -of=sambamba.p/BioD_bio_core_call.d.o -c ../BioD/bio/core/call.d [36/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_decompress.d.o.deps -of=sambamba.p/BioD_bio_core_decompress.d.o -c ../BioD/bio/core/decompress.d [37/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_genotype.d.o.deps -of=sambamba.p/BioD_bio_core_genotype.d.o -c ../BioD/bio/core/genotype.d [38/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_kmer.d.o.deps -of=sambamba.p/BioD_bio_core_kmer.d.o -c ../BioD/bio/core/kmer.d [39/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_region.d.o.deps -of=sambamba.p/BioD_bio_core_region.d.o -c ../BioD/bio/core/region.d [40/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_view.d.o.deps -of=sambamba.p/sambamba_view.d.o -c ../sambamba/view.d [41/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_tinymap.d.o.deps -of=sambamba.p/BioD_bio_core_tinymap.d.o -c ../BioD/bio/core/tinymap.d [42/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_sequence.d.o.deps -of=sambamba.p/BioD_bio_core_sequence.d.o -c ../BioD/bio/core/sequence.d [43/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_algo.d.o.deps -of=sambamba.p/BioD_bio_core_utils_algo.d.o -c ../BioD/bio/core/utils/algo.d [44/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_exception.d.o.deps -of=sambamba.p/BioD_bio_core_utils_exception.d.o -c ../BioD/bio/core/utils/exception.d [45/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_format.d.o.deps -of=sambamba.p/BioD_bio_core_utils_format.d.o -c ../BioD/bio/core/utils/format.d [46/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_memoize.d.o.deps -of=sambamba.p/BioD_bio_core_utils_memoize.d.o -c ../BioD/bio/core/utils/memoize.d [47/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_bylinefast.d.o.deps -of=sambamba.p/BioD_bio_core_utils_bylinefast.d.o -c ../BioD/bio/core/utils/bylinefast.d [48/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_outbuffer.d.o.deps -of=sambamba.p/BioD_bio_core_utils_outbuffer.d.o -c ../BioD/bio/core/utils/outbuffer.d [49/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_range.d.o.deps -of=sambamba.p/BioD_bio_core_utils_range.d.o -c ../BioD/bio/core/utils/range.d [50/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_roundbuf.d.o.deps -of=sambamba.p/BioD_bio_core_utils_roundbuf.d.o -c ../BioD/bio/core/utils/roundbuf.d [51/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_switchendianness.d.o.deps -of=sambamba.p/BioD_bio_core_utils_switchendianness.d.o -c ../BioD/bio/core/utils/switchendianness.d [52/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_stream.d.o.deps -of=sambamba.p/BioD_bio_core_utils_stream.d.o -c ../BioD/bio/core/utils/stream.d FAILED: sambamba.p/BioD_bio_core_utils_stream.d.o ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_stream.d.o.deps -of=sambamba.p/BioD_bio_core_utils_stream.d.o -c ../BioD/bio/core/utils/stream.d ../BioD/bio/core/utils/stream.d(32): Error: switch case fallthrough - use 'goto case;' if intended case "w", "wb": ^ [53/140] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -I../BioD/contrib/msgpack-d/src -enable-color -wi -release -wi -g -O2 -fcf-protection=full -g -release -boundscheck=off -enable-inlining -singleobj -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_tmpfile.d.o.deps -of=sambamba.p/BioD_bio_core_utils_tmpfile.d.o -c ../BioD/bio/core/utils/tmpfile.d ninja: build stopped: subcommand failed. dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j2 -v returned exit code 1 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 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