debspawn 0.6.5 on estragon at 2024-10-16 12:52:19 UTC-0400 dpkg-source: info: extracting rapmap in rapmap-0.15.0+dfsg dpkg-source: info: unpacking rapmap_0.15.0+dfsg.orig.tar.xz dpkg-source: info: unpacking rapmap_0.15.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-libs.patch dpkg-source: info: applying use_shared_libs.patch dpkg-source: info: applying avoid_privacy_breach.patch dpkg-source: info: applying spelling dpkg-source: info: applying portable_pause dpkg-source: info: applying no_gomp_needed dpkg-source: info: applying simde ╔═══════════════════════╗ ║ Package build ║ ╚═══════════════════════╝ Package: rapmap Version: 0.15.0+dfsg-4 Distribution: landing Architecture: arm64 Free space in workspace: 178.3GiB ┌───────────────────────────────────────┐ │ Preparing container for build │ └───────────────────────────────────────┘ Get:1 https://repo.pureos.net/pureos landing InRelease [9625 B] Fetched 9625 B in 1s (6986 B/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... build-essential is already the newest version (12.10). dpkg-dev is already the newest version (1.21.22pureos1). fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌───────────────────────────────────────────────┐ │ Installing package build-dependencies │ └───────────────────────────────────────────────┘ Note, using directory './' to get the build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils catch2 cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13t64 libbrotli1 libcereal-dev libcurl4t64 libdebhelper-perl libdivsufsort-dev libdivsufsort3 libelf1t64 libfile-stripnondeterminism-perl libfmt-dev libfmt9 libicu72 libjellyfish-2.0-2 libjellyfish-2.0-dev libjemalloc-dev libjemalloc2 libjsoncpp26 libldap-2.5-0 libmagic-mgc libmagic1t64 libncursesw6 libnghttp2-14 libpipeline1 libpkgconf3 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-stdlib libreadline8t64 librhash1 librtmp1 libsasl2-2 libsasl2-modules-db libsimde-dev libsparsehash-dev libspdlog-dev libspdlog1.12 libsqlite3-0 libssh2-1t64 libtclap-dev libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types netbase pkg-config pkgconf pkgconf-bin po-debconf procps python3 python3-importlib-metadata python3-markdown python3-typing-extensions python3-zipp python3.12 rapidjson-dev readline-common sensible-utils zlib1g-dev 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 6199 kB/45.0 MB of archives. After this operation, 187 MB of additional disk space will be used. Get:1 https://repo.pureos.net/pureos landing/main arm64 catch2 arm64 3.4.0-1 [551 kB] Get:2 https://repo.pureos.net/pureos landing/main all rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get:3 https://repo.pureos.net/pureos landing/main arm64 libcereal-dev arm64 1.3.2+dfsg-5 [221 kB] Get:4 https://repo.pureos.net/pureos landing/main arm64 libdivsufsort3 arm64 2.0.1-6 [39.1 kB] Get:5 https://repo.pureos.net/pureos landing/main arm64 libdivsufsort-dev arm64 2.0.1-6 [18.8 kB] Get:6 https://repo.pureos.net/pureos landing/main arm64 libfmt9 arm64 9.1.0+ds1-2 [107 kB] Get:7 https://repo.pureos.net/pureos landing/main arm64 libfmt-dev arm64 9.1.0+ds1-2 [171 kB] Get:8 https://repo.pureos.net/pureos landing/main arm64 libjellyfish-2.0-2 arm64 2.3.1-3+b5 [62.1 kB] Get:9 https://repo.pureos.net/pureos landing/main arm64 libjellyfish-2.0-dev arm64 2.3.1-3+b5 [136 kB] Get:10 https://repo.pureos.net/pureos landing/main arm64 libjemalloc2 arm64 5.3.0-2+b1 [218 kB] Get:11 https://repo.pureos.net/pureos landing/main arm64 libjemalloc-dev arm64 5.3.0-2+b1 [359 kB] Get:12 https://repo.pureos.net/pureos landing/main all libsimde-dev all 0.8.2-1 [465 kB] Get:13 https://repo.pureos.net/pureos landing/main all libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:14 https://repo.pureos.net/pureos landing/main arm64 libspdlog1.12 arm64 1:1.12.0+ds-2+b1 [125 kB] Get:15 https://repo.pureos.net/pureos landing/main arm64 libspdlog-dev arm64 1:1.12.0+ds-2+b1 [85.5 kB] Get:16 https://repo.pureos.net/pureos landing/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Get:17 https://repo.pureos.net/pureos landing/main all python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get:18 https://repo.pureos.net/pureos landing/main all python3-markdown all 3.7-1 [85.1 kB] Fetched 6199 kB in 3s (1890 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package media-types. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17426 files and directories currently installed.) Preparing to unpack .../00-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../01-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:arm64. Preparing to unpack .../02-libncursesw6_6.5-2_arm64.deb ... Unpacking libncursesw6:arm64 (6.5-2) ... 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Processing triggers for libc-bin (2.40-3) ... ┌───────────────┐ │ Build │ └───────────────┘ dpkg-buildpackage: info: source package rapmap dpkg-buildpackage: info: source version 0.15.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: host architecture arm64  dpkg-source --before-build .  debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/srv/build/rapmap-0.15.0+dfsg' dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam make[1]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg'  debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/srv/build/rapmap-0.15.0+dfsg' dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true .. CC: gcc CC version:  -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done version: 0.6.0 -- DISABLING NATIVE ARCH. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Making Default build type -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Found Cereal: /usr/include (Required is at least version "1.2.2") -- Cereal found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Jemalloc: /usr/lib/aarch64-linux-gnu/libjemalloc.so (found version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = .git/ CMAKE_SYSTEM_PROCESSOR: aarch64 -- Configuring done (5.5s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED JELLYFISH_ROOT  -- Build files have been written to: /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu make[1]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/srv/build/rapmap-0.15.0+dfsg' dh_auto_build cd obj-aarch64-linux-gnu && make -j32 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/srv/build/rapmap-0.15.0+dfsg -B/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/depend make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/depend make[4]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /srv/build/rapmap-0.15.0+dfsg /srv/build/rapmap-0.15.0+dfsg/src /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu 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directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make[4]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 23%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o [ 23%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o [ 23%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o [ 23%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o [ 23%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o [ 23%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o [ 26%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o [ 30%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o [ 34%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o [ 38%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/kalloc.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2_sse.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp make[4]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 38%] Built target ksw2pp_basic make[4]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 38%] Built target ksw2pp_sse2 make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /srv/build/rapmap-0.15.0+dfsg /srv/build/rapmap-0.15.0+dfsg/src /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 42%] Linking CXX static library libksw2pp.a cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 /usr/bin/ar qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o /usr/bin/ranlib libksw2pp.a make[4]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 42%] Built target ksw2pp make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/depend make[4]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /srv/build/rapmap-0.15.0+dfsg /srv/build/rapmap-0.15.0+dfsg/src /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/rapmap.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/build make[4]: Entering directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' [ 57%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o [ 57%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o [ 57%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o [ 61%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o [ 65%] Building CXX object src/CMakeFiles/rapmap.dir/HitManager.cpp.o [ 69%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o [ 69%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o [ 73%] Building CXX object src/CMakeFiles/rapmap.dir/FastxParser.cpp.o [ 80%] Building CXX object src/CMakeFiles/rapmap.dir/rank9b.cpp.o [ 80%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o [ 84%] Building C object src/CMakeFiles/rapmap.dir/bit_array.c.o cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMap.cpp.o -MF CMakeFiles/rapmap.dir/RapMap.cpp.o.d -o CMakeFiles/rapmap.dir/RapMap.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/RapMap.cpp [ 92%] Building CXX object src/CMakeFiles/rapmap.dir/edlib.cpp.o [ 92%] Building C object src/CMakeFiles/rapmap.dir/xxhash.c.o cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -MF CMakeFiles/rapmap.dir/RapMapUtils.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/RapMapUtils.cpp [ 96%] Building CXX object src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -MF CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/RapMapFileSystem.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/HitManager.cpp.o -MF CMakeFiles/rapmap.dir/HitManager.cpp.o.d -o CMakeFiles/rapmap.dir/HitManager.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/HitManager.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/FastxParser.cpp.o -MF CMakeFiles/rapmap.dir/FastxParser.cpp.o.d -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/FastxParser.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/rank9b.cpp.o -MF CMakeFiles/rapmap.dir/rank9b.cpp.o.d -o CMakeFiles/rapmap.dir/rank9b.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/rank9b.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/stringpiece.cc.o -MF CMakeFiles/rapmap.dir/stringpiece.cc.o.d -o CMakeFiles/rapmap.dir/stringpiece.cc.o -c /srv/build/rapmap-0.15.0+dfsg/src/stringpiece.cc cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/rapmap.dir/xxhash.c.o -MF CMakeFiles/rapmap.dir/xxhash.c.o.d -o CMakeFiles/rapmap.dir/xxhash.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/xxhash.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/rapmap.dir/bit_array.c.o -MF CMakeFiles/rapmap.dir/bit_array.c.o.d -o CMakeFiles/rapmap.dir/bit_array.c.o -c /srv/build/rapmap-0.15.0+dfsg/src/bit_array.c cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/edlib.cpp.o -MF CMakeFiles/rapmap.dir/edlib.cpp.o.d -o CMakeFiles/rapmap.dir/edlib.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/edlib.cpp cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/srv/build/rapmap-0.15.0+dfsg/include -I/srv/build/rapmap-0.15.0+dfsg/digestpp -I/srv/build/rapmap-0.15.0+dfsg/external -I/srv/build/rapmap-0.15.0+dfsg/external/cereal/include -I/srv/build/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -MF CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -c /srv/build/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp In file included from /srv/build/rapmap-0.15.0+dfsg/include/FastxParser.hpp:17, from /srv/build/rapmap-0.15.0+dfsg/src/FastxParser.cpp:1: /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h: In instantiation of ‘void moodycamel::details::swap_relaxed(std::atomic<_ITp>&, std::atomic<_ITp>&) [with T = std::thread::id]’: /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:3228:26: required from ‘void moodycamel::ConcurrentQueue::ImplicitProducerKVP::swap(moodycamel::ConcurrentQueue::ImplicitProducerKVP&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]’ 3228 | details::swap_relaxed(key, other.key); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:3221:4: required from ‘moodycamel::ConcurrentQueue::ImplicitProducerKVP& moodycamel::ConcurrentQueue::ImplicitProducerKVP::operator=(moodycamel::ConcurrentQueue::ImplicitProducerKVP&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]’ 3221 | swap(other); | ^~~~ /usr/include/c++/14/bits/move.h:223:11: required from ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]’ 223 | __a = _GLIBCXX_MOVE(__b); | ^ /usr/include/c++/14/bits/stl_algobase.h:185:11: required from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]’ 185 | swap(*__a, *__b); | ~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:215:16: required from ‘_ForwardIterator2 std::swap_ranges(_ForwardIterator1, _ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]’ 215 | std::iter_swap(__first1, __first2); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/array:127:25: required from ‘void std::array<_Tp, _Nm>::swap(std::array<_Tp, _Nm>&) [with _Tp = moodycamel::ConcurrentQueue, std::default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; long unsigned int _Nm = 32]’ 127 | { std::swap_ranges(begin(), end(), __other.begin()); } | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:3264:42: required from ‘void moodycamel::ConcurrentQueue::swap_implicit_producer_hashes(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]’ 3264 | initialImplicitProducerHashEntries.swap(other.initialImplicitProducerHashEntries); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:892:3: required from ‘moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::swap_internal(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]’ 892 | swap_implicit_producer_hashes(other); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:863:10: required from ‘moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::operator=(moodycamel::ConcurrentQueue&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]’ 863 | return swap_internal(other); | ^~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/FastxParser.cpp:46:14: required from ‘fastx_parser::FastxParser::FastxParser(std::vector >, std::vector >, uint32_t, uint32_t, uint32_t) [with T = fastx_parser::ReadSeq; uint32_t = unsigned int]’ 46 | readQueue_ = moodycamel::ConcurrentQueue>>( | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 |  4 * numConsumers, numParsers, 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/FastxParser.cpp:405:16: required from here 405 | template class FastxParser; | ^~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:446:19: warning: moving a temporary object prevents copy elision []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-pessimizing-move-Wpessimizing-move]8;;] 446 | T temp = std::move(left.load(std::memory_order_relaxed)); | ^~~~ /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:446:19: note: remove ‘std::move’ call /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:447:27: warning: moving a temporary object prevents copy elision []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-pessimizing-move-Wpessimizing-move]8;;] 447 | left.store(std::move(right.load(std::memory_order_relaxed)), std::memory_order_relaxed); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/concurrentqueue.h:447:27: note: remove ‘std::move’ call In file included from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /srv/build/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /srv/build/rapmap-0.15.0+dfsg/include/HitManager.hpp:25, from /srv/build/rapmap-0.15.0+dfsg/src/HitManager.cpp:22: /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 197 | registry_t() {} | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 198 | registry_t(const registry_t&) = delete; | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /srv/build/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /srv/build/rapmap-0.15.0+dfsg/src/RapMapUtils.cpp:26: /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 197 | registry_t() {} | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 198 | registry_t(const registry_t&) = delete; | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /srv/build/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:5, from /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:23: /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 197 | registry_t() {} | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 198 | registry_t(const registry_t&) = delete; | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /srv/build/rapmap-0.15.0+dfsg/include/IndexHeader.hpp:25, from /srv/build/rapmap-0.15.0+dfsg/src/RapMap.cpp:30: /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 197 | registry_t() {} | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 198 | registry_t(const registry_t&) = delete; | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /srv/build/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /srv/build/rapmap-0.15.0+dfsg/include/HitManager.hpp:25, from /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:50: /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 197 | registry_t() {} | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 198 | registry_t(const registry_t&) = delete; | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /srv/build/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /srv/build/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:50: /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 197 | registry_t() {} | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wno-template-id-cdtor-Wtemplate-id-cdtor]8;;] 198 | registry_t(const registry_t&) = delete; | ^ /srv/build/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /srv/build/rapmap-0.15.0+dfsg/include/zstr/zstr.hpp:16, from /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:62: /srv/build/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp: In static member function ‘static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const std::string&, std::ios_base::openmode)’: /srv/build/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:128:39: warning: catching polymorphic type ‘class std::ios_base::failure’ by value []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/C_002b_002b-Dialect-Options.html#index-Wcatch-value-Wcatch-value=]8;;] 128 | catch (std::ios_base::failure e) {} | ^ In file included from /srv/build/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:29: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:652:33: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 652 | duplicateNames[dupInfo.txId].push_back(processedName); | ~~~~~~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:652:33: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 652 | duplicateNames[dupInfo.txId].push_back(processedName); | ~~~~~~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from ‘bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 319 | khash[bits] = {start, stop}; | ~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:842:34: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 842 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from ‘bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 319 | khash[bits] = {start, stop}; | ~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:863:34: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 863 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = long int; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long int; Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long int]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from ‘void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]’ 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from ‘bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:839:41: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 839 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 840 |  numHashThreads); | ~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from ‘bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 319 | khash[bits] = {start, stop}; | ~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:842:34: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 842 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = int; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = int; Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = int]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from ‘void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]’ 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from ‘bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:860:41: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 860 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 861 |  numHashThreads); | ~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /srv/build/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:29: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from ‘FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >]’ 162 | l = overflow_[ind]; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from ‘bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]’ 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from ‘void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 |  saSearcher, | ~~~~~~~~~~~ 474 |  leftHCInfo); | ~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from ‘bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 |  parser, | ~~~~~~~ 767 |  std::ref(rmi), | ~~~~~~~~~~~~~~ 768 |  &iomutex, | ~~~~~~~~~ 769 |  outQueue, | ~~~~~~~~~ 770 |  std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 |  mopts); | ~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from ‘bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]’ 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 |  outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from ‘bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 319 | khash[bits] = {start, stop}; | ~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:863:34: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 863 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from ‘FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >]’ 162 | l = overflow_[ind]; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from ‘bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]’ 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from ‘void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 |  saSearcher, | ~~~~~~~~~~~ 474 |  leftHCInfo); | ~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from ‘bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 |  parser, | ~~~~~~~ 767 |  std::ref(rmi), | ~~~~~~~~~~~~~~ 768 |  &iomutex, | ~~~~~~~~~ 769 |  outQueue, | ~~~~~~~~~ 770 |  std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 |  mopts); | ~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from ‘bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]’ 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 |  outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from ‘FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >]’ 162 | l = overflow_[ind]; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from ‘bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]’ 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from ‘void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 |  saSearcher, | ~~~~~~~~~~~ 474 |  leftHCInfo); | ~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from ‘bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 |  parser, | ~~~~~~~ 767 |  std::ref(rmi), | ~~~~~~~~~~~~~~ 768 |  &iomutex, | ~~~~~~~~~ 769 |  outQueue, | ~~~~~~~~~ 770 |  std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 |  mopts); | ~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from ‘bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]’ 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 |  outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from ‘FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >]’ 162 | l = overflow_[ind]; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from ‘bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]’ 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from ‘void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 |  saSearcher, | ~~~~~~~~~~~ 474 |  leftHCInfo); | ~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from ‘bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]’ 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 |  parser, | ~~~~~~~ 767 |  std::ref(rmi), | ~~~~~~~~~~~~~~ 768 |  &iomutex, | ~~~~~~~~~ 769 |  outQueue, | ~~~~~~~~~ 770 |  std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 |  mopts); | ~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from ‘bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]’ 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 |  outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = long int; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long int; Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long int]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from ‘void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]’ 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from ‘bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:839:41: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 839 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 840 |  numHashThreads); | ~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = int; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = int; Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = int]’ 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from ‘void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]’ 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from ‘bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]’ 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:860:41: required from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 860 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 861 |  numHashThreads); | ~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 |  usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/build/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wcast-user-defined-Wcast-user-defined]8;;] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics In file included from /srv/build/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha2.hpp:9, from /srv/build/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:6, from /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:73: In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /srv/build/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /srv/build/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]’ at /srv/build/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /srv/build/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19, inlined from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]’ at /srv/build/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:581:30: /srv/build/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript ‘const long unsigned int[0]’ is partly outside array bounds of ‘unsigned char [1]’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Warray-bounds-Warray-bounds=]8;;] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /srv/build/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:5: /srv/build/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]’: /srv/build/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:169:39: note: object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ At global scope: cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics At global scope: cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics [100%] Linking CXX executable rapmap cd /srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/rapmap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/srv/build/rapmap-0.15.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wl,-z,relro -Wl,-z,now CMakeFiles/rapmap.dir/RapMap.cpp.o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o CMakeFiles/rapmap.dir/HitManager.cpp.o CMakeFiles/rapmap.dir/FastxParser.cpp.o CMakeFiles/rapmap.dir/rank9b.cpp.o CMakeFiles/rapmap.dir/stringpiece.cc.o CMakeFiles/rapmap.dir/xxhash.c.o CMakeFiles/rapmap.dir/bit_array.c.o CMakeFiles/rapmap.dir/edlib.cpp.o CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -o rapmap -L/srv/build/rapmap-0.15.0+dfsg/lib -L/srv/build/rapmap-0.15.0+dfsg/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" /usr/lib/aarch64-linux-gnu/libz.so -ldivsufsort -ldivsufsort64 -lm -lz /usr/lib/aarch64-linux-gnu/libjemalloc.so -lrt libksw2pp.a -ldl /usr/bin/ld: libksw2pp.a(KSW2Aligner.cpp.o): in function `ksw2pp::KSW2Aligner::operator()(unsigned char const*, int, unsigned char const*, int, ksw_extz_t*, ksw2pp::EnumToType<(ksw2pp::KSW2AlignmentType)2>)': ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:362:(.text+0x4a0): undefined reference to `ksw_extz2_sse2' /usr/bin/ld: ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:358:(.text+0x4d0): undefined reference to `ksw_extz2_sse41' /usr/bin/ld: libksw2pp.a(KSW2Aligner.cpp.o): in function `ksw2pp::KSW2Aligner::operator()(char const*, int, char const*, int, ksw_extz_t*, ksw2pp::EnumToType<(ksw2pp::KSW2AlignmentType)2>)': ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:227:(.text+0x101c): undefined reference to `ksw_extz2_sse2' /usr/bin/ld: ./obj-aarch64-linux-gnu/src/./src/ksw2pp/KSW2Aligner.cpp:223:(.text+0x105c): undefined reference to `ksw_extz2_sse41' collect2: error: ld returned 1 exit status make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:311: src/rapmap] Error 1 make[4]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:134: src/CMakeFiles/rapmap.dir/all] Error 2 make[3]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' make[2]: *** [Makefile:169: all] Error 2 make[2]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg/obj-aarch64-linux-gnu' dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j32 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:23: override_dh_auto_build] Error 2 make[1]: Leaving directory '/srv/build/rapmap-0.15.0+dfsg' make: *** [debian/rules:17: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 Command `dpkg-buildpackage --changes-option=-DDistribution=landing -B -mDebian Med Packaging Team -eDebian Med Packaging Team ` failed. Command debspawn build --no-buildlog --arch=arm64 --results-dir=/var/lib/lkspark/workspaces/9ad30791-929f-4b19-bf86-a54a84448b93 --only=arch --maintainer=Debian Med Packaging Team landing rapmap_0.15.0+dfsg-4.dsc failed with error code 2