############################################################################## ############################################################################## ### ### 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88129) * using platform: aarch64-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 Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Voyager/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Voyager’ version ‘1.10.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING '::' or ':::' import not declared from: ‘spatialreg’ * 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 ‘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 * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: calculateBivariate.Rd: lee, lee.mc, lee.test, localmoran_bv, BiocParallelParam, colGraphNames, colGeometryNames, localResults calculateMultivariate.Rd: localC, colGraphNames, BiocParallelParam, reducedDim calculateUnivariate.Rd: BiocParallelParam, colGeometry, annotGeometry, colGraphNames, colGeometryNames, annotGeometryNames, annotGraphNames, reducedDimNames, geometryFeatureData, colFeatureData clusterCorrelograms.Rd: BlusterParam-class, reducedDimNames clusterMoranPlot.Rd: BlusterParam-class clusterVariograms.Rd: BlusterParam-class, reducedDimNames moranPlot.Rd: colGeometryNames, geom_bin2d, geom_hex, geom_density2d plotCellBin2D.Rd: geom_bin2d, geom_hex, wrap_plots plotColDataHistogram.Rd: facet_grid plotColGraph.Rd: colGeometryNames, wrap_plots plotCorrelogram.Rd: colFeatureData, colGeometryNames, reducedDimNames, moran.test, geary.test plotGeometry.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData plotImage.Rd: wrap_plots plotLocalResult.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData, geom_bin2d, geom_hex plotMoranMC.Rd: colGeometryNames, reducedDimNames, geom_density, geom_histogram, geom_freqpoly plotSpatialFeature.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData, geom_bin2d, geom_hex plotTxBin2D.Rd: geom_bin2d, geom_hex, wrap_plots, formatTxSpots plotVariogram.Rd: colFeatureData, colGeometryNames, reducedDimNames plotVariogramMap.Rd: colGeometryNames, reducedDimNames spatialReducedDim.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData, geom_bin2d, geom_hex Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 50.184 0.853 52.156 plotImage 21.881 1.614 21.405 calculateBivariate 15.738 0.396 17.028 clusterVariograms 15.041 0.311 16.150 plotGeometry 11.853 0.371 13.733 moranPlot 10.816 0.284 11.905 plotCellBin2D 10.732 0.344 11.882 ElbowPlot 8.581 1.040 11.073 plotVariogram 6.957 0.203 7.938 spatialReducedDim 6.825 0.221 7.795 plotCrossVariogramMap 6.654 0.244 7.683 plotLocalResult 6.332 0.237 7.505 calculateUnivariate 5.795 0.306 7.009 plotColDataHistogram 5.679 0.207 6.653 plotColDataFreqpoly 5.566 0.245 6.772 plotCorrelogram 5.411 0.208 6.398 clusterMoranPlot 5.376 0.240 6.376 plotSpatialFeature 5.375 0.191 6.338 plotCrossVariogram 5.251 0.222 6.235 plotVariogramMap 5.053 0.190 6.137 * 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 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/00check.log’ for details.