############################################################################## ############################################################################## ### ### 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_1.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Voyager/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Voyager’ version ‘1.9.2’ * 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 16.494 0.227 17.495 plotImage 7.193 0.668 6.772 calculateBivariate 5.032 0.133 5.467 * 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.