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CHECK report for LineagePulse on malbec2

This page was generated on 2019-10-16 12:12:51 -0400 (Wed, 16 Oct 2019).

Package 873/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LineagePulse 1.4.0
David S Fischer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/LineagePulse
Branch: RELEASE_3_9
Last Commit: a6e92dd
Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 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

Summary

Package: LineagePulse
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2019-10-16 02:44:11 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:51:27 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 436.0 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_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/LineagePulse.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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-3.9-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 : : 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 : : 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 : : 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                                     42.030  0.080  42.112
sub-sub-LineagePulseObject-character-missing-method 18.355  0.020  18.375
getPostDrop                                         18.103  0.020  18.125
writeReport                                         17.830  0.040  18.174
cash-LineagePulseObject-method                      17.801  0.024  17.829
names-LineagePulseObject-method                     17.521  0.012  17.546
getNormData                                         17.492  0.024  17.601
accessors                                           17.104  0.378  17.497
getFitsDropout                                      16.856  0.016  16.897
getFitsMean                                         16.613  0.028  16.646
getFitsDispersion                                   16.438  0.016  16.463
sortGeneTrajectories                                14.731  0.016  14.751
runLineagePulse                                     13.306  0.008  13.315
testDropout                                         12.057  0.008  12.065
plotGene                                            11.226  0.020  11.246
* 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
accessors17.104 0.37817.497
cash-LineagePulseObject-method17.801 0.02417.829
getFitsDispersion16.438 0.01616.463
getFitsDropout16.856 0.01616.897
getFitsMean16.613 0.02816.646
getNormData17.492 0.02417.601
getPostDrop18.103 0.02018.125
names-LineagePulseObject-method17.521 0.01217.546
plotCellDensity42.030 0.08042.112
plotGene11.226 0.02011.246
runLineagePulse13.306 0.00813.315
simulateContinuousDataSet0.0350.0040.038
sortGeneTrajectories14.731 0.01614.751
sub-sub-LineagePulseObject-character-missing-method18.355 0.02018.375
testDropout12.057 0.00812.065
writeReport17.830 0.04018.174