Back to Multiple platform build/check report for BioC 3.10
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

CHECK report for LineagePulse on malbec1

This page was generated on 2020-04-15 12:13:35 -0400 (Wed, 15 Apr 2020).

Package 906/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LineagePulse 1.6.0
David S Fischer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/LineagePulse
Branch: RELEASE_3_10
Last Commit: aab186f
Last Changed Date: 2019-10-29 13:10:55 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: LineagePulse
Version: 1.6.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings LineagePulse_1.6.0.tar.gz
StartedAt: 2020-04-15 05:21:06 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:29:37 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 510.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: LineagePulse.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings LineagePulse_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/LineagePulse.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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-3.10-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                                     50.732  0.096  50.927
accessors                                           21.760  0.396  22.281
cash-LineagePulseObject-method                      20.740  0.028  20.806
sub-sub-LineagePulseObject-character-missing-method 19.264  0.032  19.366
names-LineagePulseObject-method                     18.624  0.016  18.671
getFitsDispersion                                   18.512  0.028  18.582
writeReport                                         17.988  0.028  18.051
getFitsMean                                         17.912  0.012  17.945
getFitsDropout                                      17.552  0.032  17.612
getPostDrop                                         17.332  0.032  17.398
getNormData                                         16.384  0.028  16.430
runLineagePulse                                     14.660  0.008  14.799
sortGeneTrajectories                                14.596  0.012  14.630
plotGene                                            14.508  0.016  14.546
testDropout                                         14.396  0.016  14.458
* 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-3.10-bioc/meat/LineagePulse.Rcheck/00check.log’
for details.

Installation output

LineagePulse.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL LineagePulse
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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
accessors21.760 0.39622.281
cash-LineagePulseObject-method20.740 0.02820.806
getFitsDispersion18.512 0.02818.582
getFitsDropout17.552 0.03217.612
getFitsMean17.912 0.01217.945
getNormData16.384 0.02816.430
getPostDrop17.332 0.03217.398
names-LineagePulseObject-method18.624 0.01618.671
plotCellDensity50.732 0.09650.927
plotGene14.508 0.01614.546
runLineagePulse14.660 0.00814.799
simulateContinuousDataSet0.0440.0000.042
sortGeneTrajectories14.596 0.01214.630
sub-sub-LineagePulseObject-character-missing-method19.264 0.03219.366
testDropout14.396 0.01614.458
writeReport17.988 0.02818.051