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This page was generated on 2022-01-21 13:07:58 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for LineagePulse on machv2


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.

raw results

Package 999/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LineagePulse 1.14.0  (landing page)
David S Fischer
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/LineagePulse
git_branch: RELEASE_3_14
git_last_commit: 23b2bf4
git_last_commit_date: 2021-10-26 12:40:27 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: LineagePulse
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2022-01-20 14:26:59 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:37:17 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 618.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: LineagePulse.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/LineagePulse.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.14.0’
* 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-3.14-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                                     65.939  1.509  67.541
accessors                                           23.945  0.256  24.261
getFitsDispersion                                   23.929  0.214  24.171
getFitsDropout                                      23.612  0.160  23.791
getFitsMean                                         23.536  0.125  23.681
getPostDrop                                         23.070  0.122  23.210
getNormData                                         22.979  0.146  23.161
sub-sub-LineagePulseObject-character-missing-method 22.807  0.065  22.896
writeReport                                         22.460  0.073  22.571
names-LineagePulseObject-method                     21.943  0.103  22.085
cash-LineagePulseObject-method                      21.765  0.120  21.915
sortGeneTrajectories                                16.298  0.122  16.447
testDropout                                         15.985  0.126  16.138
plotGene                                            15.918  0.111  16.047
runLineagePulse                                     15.722  0.122  15.866
* 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-3.14-bioc/meat/LineagePulse.Rcheck/00check.log’
for details.



Installation output

LineagePulse.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/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)

Tests output


Example timings

LineagePulse.Rcheck/LineagePulse-Ex.timings

nameusersystemelapsed
accessors23.945 0.25624.261
cash-LineagePulseObject-method21.765 0.12021.915
getFitsDispersion23.929 0.21424.171
getFitsDropout23.612 0.16023.791
getFitsMean23.536 0.12523.681
getNormData22.979 0.14623.161
getPostDrop23.070 0.12223.210
names-LineagePulseObject-method21.943 0.10322.085
plotCellDensity65.939 1.50967.541
plotGene15.918 0.11116.047
runLineagePulse15.722 0.12215.866
simulateContinuousDataSet0.0530.0020.054
sortGeneTrajectories16.298 0.12216.447
sub-sub-LineagePulseObject-character-missing-method22.807 0.06522.896
testDropout15.985 0.12616.138
writeReport22.460 0.07322.571