Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:38 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the LineagePulse package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1057/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LineagePulse 1.19.0 (landing page) David S Fischer
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | 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/site-library --timings LineagePulse_1.19.0.tar.gz |
StartedAt: 2023-04-12 07:05:55 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 07:14:59 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 544.7 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/site-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) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 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 loading without being on the library search path ... 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 37.193 0.164 37.358 accessors 26.413 0.316 26.730 getPostDrop 22.173 0.032 22.205 writeReport 21.990 0.092 22.082 getFitsDropout 21.848 0.124 21.973 names-LineagePulseObject-method 21.892 0.048 21.940 getFitsMean 21.618 0.068 21.687 getNormData 21.613 0.051 21.665 cash-LineagePulseObject-method 21.255 0.140 21.396 getFitsDispersion 19.486 0.064 19.550 runLineagePulse 19.122 0.080 19.202 sub-sub-LineagePulseObject-character-missing-method 19.014 0.044 19.059 sortGeneTrajectories 16.871 0.004 16.875 plotGene 16.448 0.064 16.512 testDropout 16.111 0.088 16.199 * 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/site-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 | 26.413 | 0.316 | 26.730 | |
cash-LineagePulseObject-method | 21.255 | 0.140 | 21.396 | |
getFitsDispersion | 19.486 | 0.064 | 19.550 | |
getFitsDropout | 21.848 | 0.124 | 21.973 | |
getFitsMean | 21.618 | 0.068 | 21.687 | |
getNormData | 21.613 | 0.051 | 21.665 | |
getPostDrop | 22.173 | 0.032 | 22.205 | |
names-LineagePulseObject-method | 21.892 | 0.048 | 21.940 | |
plotCellDensity | 37.193 | 0.164 | 37.358 | |
plotGene | 16.448 | 0.064 | 16.512 | |
runLineagePulse | 19.122 | 0.080 | 19.202 | |
simulateContinuousDataSet | 0.04 | 0.00 | 0.04 | |
sortGeneTrajectories | 16.871 | 0.004 | 16.875 | |
sub-sub-LineagePulseObject-character-missing-method | 19.014 | 0.044 | 19.059 | |
testDropout | 16.111 | 0.088 | 16.199 | |
writeReport | 21.990 | 0.092 | 22.082 | |