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CHECK report for LineagePulse on malbec2

This page was generated on 2019-04-09 11:49:36 -0400 (Tue, 09 Apr 2019).

Package 859/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LineagePulse 1.3.1
David S Fischer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/LineagePulse
Branch: master
Last Commit: 25d2d27
Last Changed Date: 2019-01-04 13:15:14 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: LineagePulse
Version: 1.3.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings LineagePulse_1.3.1.tar.gz
StartedAt: 2019-04-09 01:35:06 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:42:16 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 430.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: LineagePulse.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings LineagePulse_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/LineagePulse.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.3.1’
* 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-3.9-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 or elapsed time > 5s
                                                      user system elapsed
plotCellDensity                                     42.987  0.084  43.116
sub-sub-LineagePulseObject-character-missing-method 19.314  0.028  19.396
writeReport                                         18.878  0.032  18.990
getPostDrop                                         18.117  0.020  18.161
getFitsDropout                                      17.794  0.016  17.981
getFitsDispersion                                   17.488  0.024  17.570
names-LineagePulseObject-method                     17.006  0.016  17.039
accessors                                           16.223  0.235  16.595
getFitsMean                                         16.327  0.016  16.364
cash-LineagePulseObject-method                      15.380  0.019  15.404
getNormData                                         15.355  0.012  15.379
testDropout                                         13.717  0.016  13.829
runLineagePulse                                     12.310  0.024  12.358
sortGeneTrajectories                                11.975  0.008  11.983
plotGene                                            11.936  0.004  11.942
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/LineagePulse.Rcheck/00check.log’
for details.

Installation output

LineagePulse.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL LineagePulse
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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)

Tests output

Example timings

LineagePulse.Rcheck/LineagePulse-Ex.timings

nameusersystemelapsed
accessors16.223 0.23516.595
cash-LineagePulseObject-method15.380 0.01915.404
getFitsDispersion17.488 0.02417.570
getFitsDropout17.794 0.01617.981
getFitsMean16.327 0.01616.364
getNormData15.355 0.01215.379
getPostDrop18.117 0.02018.161
names-LineagePulseObject-method17.006 0.01617.039
plotCellDensity42.987 0.08443.116
plotGene11.936 0.00411.942
runLineagePulse12.310 0.02412.358
simulateContinuousDataSet0.0240.0000.024
sortGeneTrajectories11.975 0.00811.983
sub-sub-LineagePulseObject-character-missing-method19.314 0.02819.396
testDropout13.717 0.01613.829
writeReport18.878 0.03218.990