############################################################################## ############################################################################## ### ### 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_1.5.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rarr.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rarr/DESCRIPTION’ ... OK * this is package ‘Rarr’ version ‘1.5.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: 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/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/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 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... NOTE 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/4.4-arm64/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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rarr.Rcheck/00check.log’ for details.