############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:spicyR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings spicyR_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/spicyR.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spicyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spicyR’ version ‘1.8.0’ * 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 ‘spicyR’ 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 R 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 calcWeights: no visible binding for global variable ‘pairwiseAssoc’ calcWeights: no visible global function definition for ‘quantile’ inhomL: no visible binding for global variable ‘j’ inhomL: no visible binding for global variable ‘value’ inhomL: no visible binding for global variable ‘i’ inhomL: no visible binding for global variable ‘d’ inhomL: no visible binding for global variable ‘cellTypeI’ inhomL: no visible binding for global variable ‘cellTypeJ’ inhomL: no visible global function definition for ‘.’ inhomL: no visible binding for global variable ‘wt’ inhomLPair: no visible binding for global variable ‘i’ Undefined global functions or variables: . cellTypeI cellTypeJ d i j pairwiseAssoc quantile value wt Consider adding importFrom("stats", "quantile") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'SegmentedCells-class': SegmentedCells Code: function(cellData, cellProfiler = FALSE, spatialCoords = c("x", "y"), cellTypeString = "cellType", intensityString = "intensity_", morphologyString = "morphology_", phenotypeString = "phenotype_", cellIDString = "cellID", cellAnnotations = NULL, imageCellIDString = "imageCellID", imageIDString = "imageID", verbose = TRUE) Docs: function(cellData, cellProfiler = FALSE, spatialCoords = c("x", "y"), cellTypeString = "cellType", intensityString = "intensity_", morphologyString = "morphology_", phenotypeString = "phenotype_", cellIDString = "cellID", cellAnnotations = NULL, imageCellIDString = "imageCellID", imageIDString = "imageID") Argument names in code not in docs: verbose Codoc mismatches from documentation object 'getPairwise': getPairwise Code: function(cells, from = unique(cellType(cells)), to = unique(cellType(cells)), dist = NULL, window = "convex", window.length = NULL, Rs = c(20, 50, 100), sigma = NULL, minLambda = 0.05, fast = TRUE, edgeCorrect = TRUE, includeZeroCells = TRUE, BPPARAM = BiocParallel::SerialParam()) Docs: function(cells, from = unique(cellType(cells)), to = unique(cellType(cells)), dist = NULL, window = "convex", window.length = NULL, Rs = c(20, 50, 100), sigma = NULL, minLambda = 0.05, fast = TRUE, edgeCorrect = TRUE, BPPARAM = BiocParallel::SerialParam()) Argument names in code not in docs: includeZeroCells Mismatches in argument names: Position: 12 Code: includeZeroCells Docs: BPPARAM Codoc mismatches from documentation object 'SpicyResults-class': spicy Code: function(cells, condition = NULL, subject = NULL, covariates = NULL, from = NULL, to = NULL, dist = NULL, integrate = TRUE, nsim = NULL, verbose = TRUE, weights = TRUE, weightsByPair = FALSE, weightFactor = 1, window = "convex", window.length = NULL, BPPARAM = BiocParallel::SerialParam(), sigma = NULL, Rs = NULL, minLambda = 0.05, fast = TRUE, edgeCorrect = TRUE, includeZeroCells = FALSE, ...) Docs: function(cells, condition = NULL, subject = NULL, covariates = NULL, from = NULL, to = NULL, dist = NULL, integrate = TRUE, nsim = NULL, verbose = TRUE, weights = TRUE, weightsByPair = FALSE, weightFactor = 1, window = "convex", window.length = NULL, BPPARAM = BiocParallel::SerialParam(), sigma = NULL, Rs = NULL, minLambda = 0.05, fast = TRUE, edgeCorrect = TRUE, ...) Argument names in code not in docs: includeZeroCells Mismatches in argument names: Position: 22 Code: includeZeroCells Docs: ... * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getPairwise 417.132 2.312 412.639 spicy 15.791 0.048 15.238 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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, 1 NOTE See ‘/home/biocbuild/bbs-3.15-bioc/meat/spicyR.Rcheck/00check.log’ for details.