############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Voyager.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Voyager_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Voyager.Rcheck’ * using R version 4.4.3 (2025-02-28) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Voyager/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Voyager’ version ‘1.8.1’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Voyager’ can be installed ... OK * 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 ... NOTE .get_tx_df: no visible binding for global variable ‘cell_col’ .get_tx_df: no visible global function definition for ‘getTechTxFields’ .get_tx_df: no visible global function definition for ‘gdalParquetAvailable’ .get_tx_df : : no visible global function definition for ‘gdalParquetAvailable’ .get_tx_df : : no visible global function definition for ‘rowGeometryNames’ .get_tx_df : : no visible global function definition for ‘st_is_empty’ .get_tx_df : : no visible global function definition for ‘readSelectTx’ .plot_var_sf: no visible binding for global variable ‘gene’ plotTxBin2D: no visible binding for global variable ‘X’ plotTxBin2D: no visible binding for global variable ‘Y’ Undefined global functions or variables: X Y cell_col gdalParquetAvailable gene getTechTxFields readSelectTx rowGeometryNames st_is_empty * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculateMultivariate 50.444 0.975 52.582 plotImage 19.871 1.674 19.515 calculateBivariate 16.315 0.461 17.580 clusterVariograms 16.134 0.314 17.266 plotGeometry 13.103 0.422 15.077 ElbowPlot 8.714 1.047 11.333 plotCellBin2D 8.952 0.363 10.238 plotVariogram 8.799 0.218 9.826 moranPlot 8.275 0.293 9.392 plotSpatialFeature 6.788 0.209 7.793 plotLocalResult 6.424 0.242 7.712 plotCrossVariogramMap 6.366 0.250 7.395 calculateUnivariate 5.808 0.270 7.005 plotColDataHistogram 5.692 0.214 6.649 plotVariogramMap 5.696 0.207 6.846 plotColDataFreqpoly 5.627 0.241 6.780 spatialReducedDim 5.563 0.211 6.514 plotCorrelogram 5.392 0.204 6.357 plotCrossVariogram 5.346 0.228 6.353 clusterMoranPlot 4.771 0.212 5.731 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Voyager.Rcheck/00check.log’ for details.