############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rarr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rarr_1.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rarr.Rcheck’ * using R version 4.5.2 (2025-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rarr/DESCRIPTION’ ... OK * this is package ‘Rarr’ version ‘1.10.1’ * package encoding: UTF-8 * 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 hidden files and directories ... NOTE Found the following hidden files and directories: .lintr inst/extdata/zarr_examples/column-first/Unicode.zarr/.zarray inst/extdata/zarr_examples/column-first/boolean.zarr/.zarray inst/extdata/zarr_examples/column-first/float16.zarr/.zarray inst/extdata/zarr_examples/column-first/float32.zarr/.zarray inst/extdata/zarr_examples/column-first/float64.zarr/.zarray inst/extdata/zarr_examples/column-first/int16.zarr/.zarray inst/extdata/zarr_examples/column-first/int32.zarr/.zarray inst/extdata/zarr_examples/column-first/int64.zarr/.zarray inst/extdata/zarr_examples/column-first/int8.zarr/.zarray inst/extdata/zarr_examples/column-first/string.zarr/.zarray inst/extdata/zarr_examples/column-first/uint16.zarr/.zarray inst/extdata/zarr_examples/column-first/uint32.zarr/.zarray inst/extdata/zarr_examples/column-first/uint64.zarr/.zarray inst/extdata/zarr_examples/column-first/uint8.zarr/.zarray inst/extdata/zarr_examples/column-first/vlenUTF8.zarr/.zarray inst/extdata/zarr_examples/compression/bzip2.zarr/.zarray inst/extdata/zarr_examples/compression/lz4.zarr/.zarray inst/extdata/zarr_examples/compression/lzma.zarr/.zarray inst/extdata/zarr_examples/compression/zlib.zarr/.zarray inst/extdata/zarr_examples/compression/zstd.zarr/.zarray inst/extdata/zarr_examples/fill-values/double-inf.zarr/.zarray inst/extdata/zarr_examples/fill-values/double-neginf.zarr/.zarray inst/extdata/zarr_examples/metadata/complex_consolidated.zarr/.zmetadata inst/extdata/zarr_examples/metadata/consolidated.zarr/.zattrs inst/extdata/zarr_examples/metadata/consolidated.zarr/.zgroup inst/extdata/zarr_examples/metadata/consolidated.zarr/.zmetadata inst/extdata/zarr_examples/metadata/consolidated.zarr/a/.zarray inst/extdata/zarr_examples/metadata/consolidated.zarr/a/.zattrs inst/extdata/zarr_examples/metadata/consolidated.zarr/b/.zarray inst/extdata/zarr_examples/metadata/consolidated.zarr/b/.zattrs inst/extdata/zarr_examples/metadata/consolidated.zarr/c/.zarray inst/extdata/zarr_examples/metadata/consolidated.zarr/c/.zattrs inst/extdata/zarr_examples/metadata/invalid_mixed.zarr/.zarray inst/extdata/zarr_examples/metadata/invalid_mixed.zarr/.zattrs inst/extdata/zarr_examples/row-first/float16.zarr/.zarray inst/extdata/zarr_examples/row-first/float32.zarr/.zarray inst/extdata/zarr_examples/row-first/float64.zarr/.zarray inst/extdata/zarr_examples/row-first/int16.zarr/.zarray inst/extdata/zarr_examples/row-first/int32.zarr/.zarray inst/extdata/zarr_examples/row-first/int64.zarr/.zarray inst/extdata/zarr_examples/row-first/int8.zarr/.zarray inst/extdata/zarr_examples/row-first/other.zarr/.zarray inst/extdata/zarr_examples/row-first/string.zarr/.zarray inst/extdata/zarr_examples/row-first/uint32.zarr/.zarray inst/extdata/zarr_examples/row-first/uint64.zarr/.zarray inst/extdata/zarr_examples/row-first/uint8.zarr/.zarray These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rarr’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... INFO GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rarr/libs/Rarr.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed compressors 0.541 0.249 7.838 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rarr.Rcheck/00check.log’ for details.