############################################################################## ############################################################################## ### ### 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/LineagePulse.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘LineagePulse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘LineagePulse’ version ‘1.16.0’ * 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-3.15-bioc/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 72.621 1.259 73.991 accessors 27.435 0.279 27.784 getNormData 27.412 0.099 27.545 getFitsMean 27.269 0.102 27.433 getPostDrop 27.227 0.116 27.392 getFitsDispersion 27.149 0.152 27.455 getFitsDropout 27.179 0.114 27.366 sub-sub-LineagePulseObject-character-missing-method 26.922 0.066 27.030 writeReport 26.789 0.065 26.899 names-LineagePulseObject-method 26.559 0.085 26.687 cash-LineagePulseObject-method 26.463 0.107 26.823 sortGeneTrajectories 19.184 0.106 19.312 testDropout 19.158 0.118 19.305 plotGene 18.826 0.109 18.961 runLineagePulse 18.596 0.122 18.745 * 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-3.15-bioc/meat/LineagePulse.Rcheck/00check.log’ for details.