* installing *source* package ‘N2R’ ... ** this is package ‘N2R’ version ‘1.0.4’ ** using staged installation ** libs using C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’ clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -I"./n2/include" -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -I"./n2/include" -fpic -g -O3 -Wall -pedantic -c check_openmp.cpp -o check_openmp.o clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"../inst/include" -I"./n2/include" -fpic -g -O3 -Wall -pedantic -c n2knn.cpp -o n2knn.o In file included from n2knn.cpp:24: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from n2knn.cpp:24: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from n2knn.cpp:24: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from n2knn.cpp:24: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. (cd n2 && CFLAGS="-g -O3 -Wall -pedantic" CXXFLAGS="-g -O3 -Wall -pedantic " MAKE="make -f \"/home/hornik/tmp/R-d-clang-21/etc/Makeconf\" -f Makefile" make -f "/home/hornik/tmp/R-d-clang-21/etc/Makeconf" -f Makefile lib) || exit 1; make[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/N2R.Rcheck/00_pkg_src/N2R/src/n2' clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./include" -fpic -g -O3 -Wall -pedantic -c base.cc -o base.o clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./include" -fpic -g -O3 -Wall -pedantic -c hnsw.cc -o hnsw.o In file included from hnsw.cc:28: ./include/n2/hnsw.h:163:15: warning: private field 'memory_per_higher_level_' is not used [-Wunused-private-field] 163 | long long memory_per_higher_level_ = 0; | ^ 1 warning generated. clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./include" -fpic -g -O3 -Wall -pedantic -c hnsw_node.cc -o hnsw_node.o clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./include" -fpic -g -O3 -Wall -pedantic -c distance.cc -o distance.o clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./include" -fpic -g -O3 -Wall -pedantic -c heuristic.cc -o heuristic.o clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I"./include" -fpic -g -O3 -Wall -pedantic -c mmap.cc -o mmap.o ar rvs ../libn2.a base.o hnsw.o hnsw_node.o distance.o heuristic.o mmap.o ar: creating ../libn2.a a - base.o a - hnsw.o a - hnsw_node.o a - distance.o a - heuristic.o a - mmap.o make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/N2R.Rcheck/00_pkg_src/N2R/src/n2' clang++-21 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-clang-21/lib -Wl,-O1 -o N2R.so RcppExports.o check_openmp.o n2knn.o -L. -lpthread -ln2 -lm Usage: Rscript [options] file [args] or: Rscript [options] -e expr [-e expr2 ...] [args] A binary front-end to R, for use in scripting applications. Options: --help Print usage and exit --version Print version and exit --verbose Print information on progress --default-packages=LIST Attach these packages on startup; a comma-separated LIST of package names, or 'NULL' and options to R (in addition to --no-echo --no-restore), for example: --save Do save workspace at the end of the session --no-environ Don't read the site and user environment files --no-site-file Don't read the site-wide Rprofile --no-init-file Don't read the user R profile --restore Do restore previously saved objects at startup --vanilla Combine --no-save, --no-restore, --no-site-file, --no-init-file and --no-environ Expressions (one or more '-e ') may be used *instead* of 'file'. Any additional 'args' can be accessed from R via 'commandArgs(TRUE)'. See also ?Rscript from within R. -llapack -L/home/hornik/tmp/R-d-clang-21/lib -lRblas -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R-d-clang-21/lib -lR clang++-21: error: unknown argument: '--default-packages=LIST' clang++-21: error: unknown argument: '--no-echo' clang++-21: error: unknown argument: '--no-restore),' clang++-21: error: unknown argument: '--save' clang++-21: error: unknown argument: '--no-environ' clang++-21: error: unknown argument: '--no-site-file' clang++-21: error: unknown argument: '--no-init-file' clang++-21: error: unknown argument: '--restore' clang++-21: error: unknown argument: '--vanilla' clang++-21: error: unknown argument: '--no-save,' clang++-21: error: unknown argument: '--no-restore,' clang++-21: error: unknown argument: '--no-site-file,' clang++-21: error: unknown argument: '--no-init-file' clang++-21: error: unknown argument: '--no-environ' OVERVIEW: clang LLVM compiler USAGE: clang [options] file... OPTIONS: -### Print (but do not run) the commands to run for this compilation --analyzer-output Static analyzer report output format (html|plist|plist-multi-file|plist-html|sarif|sarif-html|text). --analyze Run the static analyzer -B Search $prefix$file for executables, libraries, and data files. If $prefix is a directory, search $prefix/$file -b Pass -b to the linker on AIX -CC Include comments from within macros in preprocessed output -cl-denorms-are-zero OpenCL only. Allow denormals to be flushed to zero. -cl-ext= OpenCL only. Enable or disable OpenCL extensions/optional features. The argument is a comma-separated sequence of one or more extension names, each prefixed by '+' or '-'. -cl-fast-relaxed-math OpenCL only. Sets -cl-finite-math-only and -cl-unsafe-math-optimizations, and defines __FAST_RELAXED_MATH__. -cl-finite-math-only OpenCL only. Allow floating-point optimizations that assume arguments and results are not NaNs or +-Inf. -cl-fp32-correctly-rounded-divide-sqrt OpenCL only. Specify that single precision floating-point divide and sqrt used in the program source are correctly rounded. -cl-kernel-arg-info OpenCL only. Generate kernel argument metadata. -cl-mad-enable OpenCL only. Allow use of less precise MAD computations in the generated binary. -cl-no-signed-zeros OpenCL only. Allow use of less precise no signed zeros computations in the generated binary. -cl-no-stdinc OpenCL only. Disables all standard includes containing non-native compiler types and functions. -cl-opt-disable OpenCL only. This option disables all optimizations. By default optimizations are enabled. -cl-single-precision-constant OpenCL only. Treat double precision floating-point constant as single precision constant. -cl-std= OpenCL language standard to compile for. -cl-strict-aliasing OpenCL only. This option is added for compatibility with OpenCL 1.0. -cl-uniform-work-group-size OpenCL only. Defines that the global work-size be a multiple of the work-group size specified to clEnqueueNDRangeKernel -cl-unsafe-math-optimizations OpenCL only. Allow unsafe floating-point optimizations. Also implies -cl-no-signed-zeros and -cl-mad-enable. -clangir-disable-passes Disable CIR transformations pipeline -clangir-disable-verifier ClangIR: Disable MLIR module verifier --config= Specify configuration file --cuda-compile-host-device Compile CUDA code for both host and device (default). Has no effect on non-CUDA compilations. --cuda-device-only Compile CUDA code for device only --cuda-feature= Manually specify the CUDA feature to use --cuda-host-only Compile CUDA code for host only. Has no effect on non-CUDA compilations. --cuda-include-ptx= Include PTX for the following GPU architecture (e.g. sm_35) or 'all'. May be specified more than once. --cuda-noopt-device-debug Enable device-side debug info generation. Disables ptxas optimizations. --cuda-path-ignore-env Ignore environment variables to detect CUDA installation --cuda-path= CUDA installation path -cuid= An ID for compilation unit, which should be the same for the same compilation unit but different for different compilation units. It is used to externalize device-side static variables for single source offloading languages CUDA and HIP so that they can be accessed by the host code of the same compilation unit. -cxx-isystem Add directory to the C++ SYSTEM include search path -C Include comments in preprocessed output -c Only run preprocess, compile, and assemble steps -darwin-target-variant-triple Specify the darwin target variant triple -darwin-target-variant Generate code for an additional runtime variant of the deployment target -dD Print macro definitions in -E mode in addition to normal output -dependency-dot Filename to write DOT-formatted header dependencies to -dependency-file Filename (or -) to write dependency output to -dI Print include directives in -E mode in addition to normal output -dM Print macro definitions in -E mode instead of normal output -dsym-dir Directory to output dSYM's (if any) to -dumpdir Use as a prefix to form auxiliary and dump file names -dumpmachine Display the compiler's target processor -dumpversion Display the version of the compiler -D = Define to (or 1 if omitted) --embed-dir= Add directory to embed search path -emit-ast Emit Clang AST files for source inputs -emit-cir Build ASTs and then lower to ClangIR --emit-extension-symbol-graphs Generate additional symbol graphs for extended modules. -emit-interface-stubs Generate Interface Stub Files. -emit-llvm Use the LLVM representation for assembler and object files -emit-merged-ifs Generate Interface Stub Files, emit merged text not binary. --emit-static-lib Enable linker job to emit a static library. -emit-symbol-graph Generate Extract API information as a side effect of compilation. --end-no-unused-arguments Start emitting warnings for unused driver arguments --extract-api-ignores= Comma separated list of files containing a new line separated list of API symbols to ignore when extracting API information. -extract-api Extract API information -E Only run the preprocessor -faapcs-bitfield-load Follows the AAPCS standard that all volatile bit-field write generates at least one load. (ARM only). -faapcs-bitfield-width Follow the AAPCS standard requirement stating that volatile bit-field width is dictated by the field container type. (ARM only). -faarch64-jump-table-hardening Use hardened lowering for jump-table dispatch -faddrsig Emit an address-significance table -falign-loops= N must be a power of two. Align loops to the boundary -faligned-allocation Enable C++17 aligned allocation functions -fallow-editor-placeholders Treat editor placeholders as valid source code -fallow-runtime-check-skip-hot-cutoff= Exclude __builtin_allow_runtime_check for the top hottest code responsible for the given fraction of PGO counters (0.0 [default] = skip none; 1.0 = skip all). Argument format: -faltivec-src-compat= Source-level compatibility for Altivec vectors (for PowerPC targets). This includes results of vector comparison (scalar for 'xl', vector for 'gcc') as well as behavior when initializing with a scalar (splatting for 'xl', element zero only for 'gcc'). For 'mixed', the compatibility is as 'gcc' for 'vector bool/vector pixel' and as 'xl' for other types. Current default is 'mixed'. -fansi-escape-codes Use ANSI escape codes for diagnostics -fapinotes-modules Enable module-based external API notes support -fapinotes-swift-version= Specify the Swift version to use when filtering API notes -fapinotes Enable external API notes support -fapple-kext Use Apple's kernel extensions ABI -fapple-link-rtlib Force linking the clang builtins runtime library -fapple-pragma-pack Enable Apple gcc-compatible #pragma pack handling -fapplication-extension Restrict code to those available for App Extensions -fapprox-func Allow certain math function calls to be replaced with an approximately equivalent calculation -fassume-nothrow-exception-dtor Assume that exception objects' destructors are non-throwing -fasync-exceptions Enable EH Asynchronous exceptions -fatomic-fine-grained-memory May have atomic operations on fine-grained memory -fatomic-ignore-denormal-mode Allow atomic operations to ignore denormal mode -fatomic-remote-memory May have atomic operations on remote memory -fauto-import MinGW specific. Enable code generation support for automatic dllimport, and enable support for it in the linker. Enabled by default. -fbasic-block-address-map Emit the basic block address map section. -fbasic-block-sections= Place each function's basic blocks in unique sections (ELF Only) -fbinutils-version= Produced object files can use all ELF features supported by this binutils version and newer. If -fno-integrated-as is specified, the generated assembly will consider GNU as support. 'none' means that all ELF features can be used, regardless of binutils support. Defaults to 2.26. -fblocks Enable the 'blocks' language feature -fborland-extensions Accept non-standard constructs supported by the Borland compiler -fbuild-session-file= Use the last modification time of as the build session timestamp -fbuild-session-timestamp=