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This page was generated on 2021-10-15 15:06:40 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the LineagePulse package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LineagePulse.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 987/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LineagePulse 1.12.0 (landing page) David S Fischer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: LineagePulse |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LineagePulse_1.12.0.tar.gz |
StartedAt: 2021-10-14 20:29:27 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:38:51 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 564.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: LineagePulse.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LineagePulse_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/LineagePulse.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.12.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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-3.13-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 : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 61.555 1.311 62.916 accessors 21.742 0.185 21.955 cash-LineagePulseObject-method 21.241 0.091 21.354 getNormData 21.004 0.109 21.132 sub-sub-LineagePulseObject-character-missing-method 20.995 0.061 21.073 getFitsDropout 20.849 0.154 21.018 writeReport 20.922 0.055 20.991 getFitsDispersion 20.366 0.175 20.566 testDropout 20.219 0.057 20.291 names-LineagePulseObject-method 20.166 0.082 20.270 getFitsMean 20.092 0.144 20.272 sortGeneTrajectories 19.991 0.059 20.062 runLineagePulse 19.675 0.066 19.761 plotGene 19.199 0.053 19.268 getPostDrop 18.307 0.155 18.479 * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/LineagePulse.Rcheck/00check.log’ for details.
LineagePulse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LineagePulse ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘LineagePulse’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading 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) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (LineagePulse)
LineagePulse.Rcheck/LineagePulse-Ex.timings
name | user | system | elapsed | |
accessors | 21.742 | 0.185 | 21.955 | |
cash-LineagePulseObject-method | 21.241 | 0.091 | 21.354 | |
getFitsDispersion | 20.366 | 0.175 | 20.566 | |
getFitsDropout | 20.849 | 0.154 | 21.018 | |
getFitsMean | 20.092 | 0.144 | 20.272 | |
getNormData | 21.004 | 0.109 | 21.132 | |
getPostDrop | 18.307 | 0.155 | 18.479 | |
names-LineagePulseObject-method | 20.166 | 0.082 | 20.270 | |
plotCellDensity | 61.555 | 1.311 | 62.916 | |
plotGene | 19.199 | 0.053 | 19.268 | |
runLineagePulse | 19.675 | 0.066 | 19.761 | |
simulateContinuousDataSet | 0.047 | 0.003 | 0.050 | |
sortGeneTrajectories | 19.991 | 0.059 | 20.062 | |
sub-sub-LineagePulseObject-character-missing-method | 20.995 | 0.061 | 21.073 | |
testDropout | 20.219 | 0.057 | 20.291 | |
writeReport | 20.922 | 0.055 | 20.991 | |