############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LineagePulse_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/LineagePulse.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘LineagePulse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘LineagePulse’ version ‘1.20.0’ * 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 ‘LineagePulse’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = matDispParam, matDropParam = matDropParam, matWeights = matWeights) Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)), matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)), matWeights = matWeights) See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/LineagePulse.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 decompressDispByGeneMM: no visible binding for global variable ‘lsDispModel’ evalLogLikMatrix : : possible error in evalLogLikGeneMM(vecCounts = vecCounts, matMuParam = matMuParam, vecNormConst = lsMuModel$lsMuModelGlobal$vecNormConst, matDispParam = matDispParam, matDropParam = matDropParam, matWeights = matWeights, vecidxNotZero = which(!is.na(vecCounts) & vecCounts > 0), vecidxZero = which(!is.na(vecCounts) & vecCounts == 0), scaNCells = length(vecCounts)): unused arguments (matDispParam = matDispParam, matDropParam = matDropParam, matWeights = matWeights) evalLogLikMatrix : : possible error in evalLogLikGeneMM(vecCounts = vecCounts, matMuParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecMuParam)), vecNormConst = lsMuModel$lsMuModelGlobal$vecNormConst, matDispParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)), matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)), matWeights = matWeights, vecidxNotZero = which(!is.na(vecCounts) & vecCounts > 0), vecidxZero = which(!is.na(vecCounts) & vecCounts == 0), : unused arguments (matDispParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)), matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)), matWeights = matWeights) evalLogLikMatrix : : possible error in scaNCells = length(vecCounts)): unused arguments (matDispParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)), matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)), matWeights = matWeights) plotCellDensity: no visible binding for global variable ‘continuous’ plotGene: no visible binding for global variable ‘x’ plotGene: no visible binding for global variable ‘dropout_posterior’ plotGene: no visible binding for global variable ‘groups’ plotGene: no visible binding for global variable ‘dfAnnot’ plotGene: no visible binding for global variable ‘mean_count’ plotGene: no visible binding for global variable ‘quantile_25’ plotGene: no visible binding for global variable ‘quantile_75’ plotGene: no visible binding for global variable ‘model’ plotGene: no visible binding for global variable ‘continuous’ plotGene: no visible binding for global variable ‘trajectory_contour’ plotGene: no visible binding for global variable ‘ncells’ Undefined global functions or variables: continuous dfAnnot dropout_posterior groups lsDispModel mean_count model ncells quantile_25 quantile_75 trajectory_contour x * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotCellDensity 40.421 1.414 63.067 accessors 18.552 0.154 28.688 sub-sub-LineagePulseObject-character-missing-method 16.836 0.210 26.008 writeReport 16.798 0.137 25.476 cash-LineagePulseObject-method 16.463 0.124 25.368 names-LineagePulseObject-method 16.316 0.120 25.197 getFitsDispersion 16.022 0.193 25.068 getFitsMean 15.990 0.178 24.827 getFitsDropout 15.956 0.179 24.634 getNormData 15.946 0.184 24.399 getPostDrop 15.917 0.180 22.705 sortGeneTrajectories 13.298 0.195 20.874 testDropout 13.316 0.167 20.698 plotGene 12.951 0.171 20.151 runLineagePulse 12.940 0.165 20.112 * 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 ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/LineagePulse.Rcheck/00check.log’ for details.