Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:11 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1029/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LineagePulse 1.19.0 (landing page) David S Fischer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: LineagePulse |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings LineagePulse_1.19.0.tar.gz |
StartedAt: 2023-02-07 06:14:26 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 06:24:56 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 629.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: LineagePulse.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings LineagePulse_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/LineagePulse.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘LineagePulse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘LineagePulse’ version ‘1.19.0’ * 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 ‘/home/biocbuild/bbs-3.17-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 51.901 0.040 56.094 accessors 23.953 0.276 25.475 sub-sub-LineagePulseObject-character-missing-method 22.402 0.000 24.139 writeReport 21.894 0.000 22.641 names-LineagePulseObject-method 21.585 0.004 21.608 cash-LineagePulseObject-method 21.326 0.008 21.473 getNormData 20.571 0.268 21.550 getFitsDropout 20.603 0.032 20.713 getPostDrop 20.564 0.008 20.613 getFitsMean 20.563 0.004 20.660 getFitsDispersion 20.446 0.016 20.494 testDropout 16.997 0.004 17.843 sortGeneTrajectories 16.908 0.012 18.546 runLineagePulse 16.609 0.004 18.289 plotGene 16.454 0.019 16.642 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘LineagePulse_Tutorial.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/LineagePulse.Rcheck/00check.log’ for details.
LineagePulse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL LineagePulse ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 23.953 | 0.276 | 25.475 | |
cash-LineagePulseObject-method | 21.326 | 0.008 | 21.473 | |
getFitsDispersion | 20.446 | 0.016 | 20.494 | |
getFitsDropout | 20.603 | 0.032 | 20.713 | |
getFitsMean | 20.563 | 0.004 | 20.660 | |
getNormData | 20.571 | 0.268 | 21.550 | |
getPostDrop | 20.564 | 0.008 | 20.613 | |
names-LineagePulseObject-method | 21.585 | 0.004 | 21.608 | |
plotCellDensity | 51.901 | 0.040 | 56.094 | |
plotGene | 16.454 | 0.019 | 16.642 | |
runLineagePulse | 16.609 | 0.004 | 18.289 | |
simulateContinuousDataSet | 0.037 | 0.000 | 0.053 | |
sortGeneTrajectories | 16.908 | 0.012 | 18.546 | |
sub-sub-LineagePulseObject-character-missing-method | 22.402 | 0.000 | 24.139 | |
testDropout | 16.997 | 0.004 | 17.843 | |
writeReport | 21.894 | 0.000 | 22.641 | |