* using log directory ‘/srv/hornik/tmp/CRAN/RcppPlanc.Rcheck’ * using R Under development (unstable) (2023-11-01 r85459) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (16) GNU Fortran (Debian 13.2.0-5) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘RcppPlanc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RcppPlanc’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Andrew Robbins ’ New submission Possibly misspelled words in DESCRIPTION: Eswar (16:14) Gao (19:14) Kannan (15:14) Kriebel (20:14) NMF (14:29) NTF (14:33) Nonnegativity (3:45) Welch (18:14, 20:24) al (15:25, 16:24, 18:23, 19:21) et (15:21, 16:20, 18:20, 19:18) * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘RcppPlanc’ can be installed ... [67s/66s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘CMakeLists.txt’ ‘cmake’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Found the following directory with the name of a version control directory: ./src/_deps/highfive-src/.git These should not be in a package tarball. * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] WARNING Error loading dataset 'ctrl.sparse': Error in .requirePackage(package) : unable to find required package 'Matrix' Error loading dataset 'stim.sparse': Error in .requirePackage(package) : unable to find required package 'Matrix' The dataset(s) may use package(s) not declared in Depends/Imports. * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... NOTE Found the following sources/headers not terminated with a newline: src/_deps/highfive-build/CMakeFiles/hdf5/cmake_hdf5_test.c src/_deps/highfive-src/deps/catch2/tests/SelfTest/UsageTests/MatchersRanges.tests.cpp src/_deps/highfive-src/include/highfive/bits/H5Friends.hpp Some compilers warn on such files. * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: src/Makefile src/_deps/highfive-build/Makefile src/_deps/highfive-src/src/benchmarks/Makefile src/_deps/highfive-subbuild/Makefile Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking pragmas in C/C++ headers and code ... WARNING Files which contain non-portable pragma(s) ‘src/_deps/highfive-src/deps/catch2/extras/catch_amalgamated.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/internal/catch_reusable_string_stream.hpp’ Files which contain pragma(s) suppressing diagnostics: ‘src/_deps/highfive-src/deps/catch2/examples/231-Cfg-OutputStreams.cpp’ ‘src/_deps/highfive-src/deps/catch2/extras/catch_amalgamated.cpp’ ‘src/_deps/highfive-src/deps/catch2/extras/catch_amalgamated.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/catch_template_test_macros.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/catch_test_case_info.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/catch_test_spec.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/internal/catch_reusable_string_stream.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/internal/catch_template_test_registry.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/internal/catch_test_macro_impl.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/internal/catch_test_registry.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/internal/catch_test_spec_parser.hpp’ ‘src/_deps/highfive-src/deps/catch2/src/catch2/matchers/catch_matchers_floating_point.cpp’ ‘src/_deps/highfive-src/deps/catch2/tests/ExtraTests/X02-DisabledMacros.cpp’ ‘src/_deps/highfive-src/deps/catch2/tests/SelfTest/UsageTests/Compilation.tests.cpp’ ‘src/_deps/highfive-src/deps/catch2/tests/SelfTest/UsageTests/Condition.tests.cpp’ ‘src/_deps/highfive-src/deps/catch2/tests/SelfTest/UsageTests/Exception.tests.cpp’ ‘src/_deps/highfive-src/deps/catch2/tests/SelfTest/UsageTests/Generators.tests.cpp’ ‘src/_deps/highfive-src/deps/catch2/tests/SelfTest/UsageTests/Message.tests.cpp’ ‘src/_deps/highfive-src/deps/catch2/tests/SelfTest/UsageTests/Tricky.tests.cpp’ * checking compilation flags used ... NOTE Compilation used the following non-portable flag(s): ‘-freciprocal-math’ ‘-funsafe-math-optimizations’ * checking compiled code ... NOTE Note: information on .o files is not available File ‘/srv/hornik/tmp/CRAN/RcppPlanc.Rcheck/RcppPlanc/libs/RcppPlanc.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Found ‘abort’, possibly from ‘abort’ (C) Found ‘srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [25s/2s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed inmf 6.312 0.429 0.827 onlineINMF 5.087 0.210 0.240 Examples with CPU time > 2.5 times elapsed time user system elapsed ratio onlineINMF 5.087 0.210 0.240 22.071 inmf 6.312 0.429 0.827 8.151 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [746s/25s] NOTE Running ‘testthat.R’ [746s/25s] Running R code in ‘testthat.R’ had CPU time 29.7 times elapsed time * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [48s/3s] NOTE Re-building vignettes had CPU time 14.4 times elapsed time * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 8 NOTEs