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CHECK report for LineagePulse on tokay2

This page was generated on 2020-10-17 11:56:57 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE LineagePulse PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 939/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LineagePulse 1.8.0
David S Fischer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/LineagePulse
Branch: RELEASE_3_11
Last Commit: 13f0ec8
Last Changed Date: 2020-04-27 15:12:36 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: LineagePulse
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LineagePulse_1.8.0.tar.gz
StartedAt: 2020-10-17 05:31:09 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:44:52 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 822.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: LineagePulse.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LineagePulse_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/LineagePulse.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LineagePulse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LineagePulse' version '1.8.0'
* 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 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 'C:/Users/biocbuild/bbs-3.11-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     44.63   0.10   44.72
cash-LineagePulseObject-method                      19.72   0.00   19.71
getFitsMean                                         18.48   0.00   18.48
getFitsDispersion                                   17.73   0.02   17.75
accessors                                           17.28   0.12   17.43
writeReport                                         17.00   0.00   17.00
getPostDrop                                         16.15   0.03   16.19
sub-sub-LineagePulseObject-character-missing-method 15.73   0.19   15.92
getNormData                                         15.82   0.06   15.88
getFitsDropout                                      14.83   0.05   14.88
names-LineagePulseObject-method                     14.64   0.01   14.67
testDropout                                         12.61   0.00   12.62
plotGene                                            12.11   0.00   12.11
runLineagePulse                                     11.84   0.00   11.84
sortGeneTrajectories                                10.60   0.00   10.60
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     46.38   0.08   46.45
getFitsDispersion                                   24.00   0.06   24.20
accessors                                           22.59   0.01   22.62
writeReport                                         21.50   0.00   21.52
sub-sub-LineagePulseObject-character-missing-method 20.93   0.06   20.98
getNormData                                         19.53   0.00   19.54
names-LineagePulseObject-method                     19.36   0.03   19.39
cash-LineagePulseObject-method                      19.30   0.05   19.34
getFitsDropout                                      19.28   0.02   19.30
getPostDrop                                         19.16   0.02   19.17
getFitsMean                                         18.79   0.01   18.81
testDropout                                         16.87   0.01   16.89
sortGeneTrajectories                                15.23   0.00   15.24
runLineagePulse                                     14.64   0.02   14.66
plotGene                                            14.42   0.00   14.42
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.

Installation output

LineagePulse.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/LineagePulse_1.8.0.tar.gz && rm -rf LineagePulse.buildbin-libdir && mkdir LineagePulse.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LineagePulse.buildbin-libdir LineagePulse_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL LineagePulse_1.8.0.zip && rm LineagePulse_1.8.0.tar.gz LineagePulse_1.8.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 74622  100 74622    0     0   963k      0 --:--:-- --:--:-- --:--:-- 1056k

install for i386

* 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
  converting help for package 'LineagePulse'
    finding HTML links ... done
    LPsetters                               html  
    LineagePulseObject-class                html  
    accessors                               html  
    calcNormConst                           html  
    calcPostDrop_Matrix                     html  
    calcPostDrop_Vector                     html  
    cash-LineagePulseObject-method          html  
    decompressDispByGene                    html  
    decompressDispByGeneMM                  html  
    decompressDropoutRateByCell             html  
    decompressDropoutRateByGene             html  
    decompressMeansByGene                   html  
    decompressMuByGeneMM                    html  
    evalDropoutModel                        html  
    evalDropoutModel_comp                   html  
    evalImpulseModel                        html  
    evalImpulseModel_comp                   html  
    evalLogLikGene                          html  
    evalLogLikGeneMM                        html  
    evalLogLikMatrix                        html  
    evalLogLikMuDispGeneFit                 html  
    evalLogLikMuDispGeneFit_comp            html  
    evalLogLikNB                            html  
    evalLogLikNB_comp                       html  
    evalLogLikPiZINB_ManyCells              html  
    evalLogLikPiZINB_ManyCells_comp         html  
    evalLogLikPiZINB_SingleCell             html  
    evalLogLikPiZINB_SingleCell_comp        html  
    evalLogLikZINB                          html  
    evalLogLikZINB_comp                     html  
    fitLPModels                             html  
    fitModel                                html  
    fitMuDisp                               html  
    fitMuDispGene                           html  
    fitMuDispGeneImpulse                    html  
    fitMuDispGeneMM                         html  
    fitPi                                   html  
    fitPi_ManyCells                         html  
    fitPi_SingleCell                        html  
    getFitsDispersion                       html  
    getFitsDropout                          html  
    getFitsMean                             html  
    getNormData                             html  
    getPostDrop                             html  
    initDispModel                           html  
    initDropModel                           html  
    initMuModel                             html  
    initialiseImpulseParameters             html  
    names-LineagePulseObject-method         html  
    plotCellDensity                         html  
    plotGene                                html  
    processSCData                           html  
    runDEAnalysis                           html  
    runLineagePulse                         html  
    simulateContinuousDataSet               html  
    sortGeneTrajectories                    html  
    sub-sub-LineagePulseObject-character-missing-method
                                            html  
    testDropout                             html  
    writeReport                             html  
** 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

install for x64

* installing *source* package 'LineagePulse' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LineagePulse' as LineagePulse_1.8.0.zip
* DONE (LineagePulse)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'LineagePulse' successfully unpacked and MD5 sums checked

Tests output

Example timings

LineagePulse.Rcheck/examples_i386/LineagePulse-Ex.timings

nameusersystemelapsed
accessors17.28 0.1217.43
cash-LineagePulseObject-method19.72 0.0019.71
getFitsDispersion17.73 0.0217.75
getFitsDropout14.83 0.0514.88
getFitsMean18.48 0.0018.48
getNormData15.82 0.0615.88
getPostDrop16.15 0.0316.19
names-LineagePulseObject-method14.64 0.0114.67
plotCellDensity44.63 0.1044.72
plotGene12.11 0.0012.11
runLineagePulse11.84 0.0011.84
simulateContinuousDataSet0.030.000.03
sortGeneTrajectories10.6 0.010.6
sub-sub-LineagePulseObject-character-missing-method15.73 0.1915.92
testDropout12.61 0.0012.62
writeReport17 017

LineagePulse.Rcheck/examples_x64/LineagePulse-Ex.timings

nameusersystemelapsed
accessors22.59 0.0122.62
cash-LineagePulseObject-method19.30 0.0519.34
getFitsDispersion24.00 0.0624.20
getFitsDropout19.28 0.0219.30
getFitsMean18.79 0.0118.81
getNormData19.53 0.0019.54
getPostDrop19.16 0.0219.17
names-LineagePulseObject-method19.36 0.0319.39
plotCellDensity46.38 0.0846.45
plotGene14.42 0.0014.42
runLineagePulse14.64 0.0214.66
simulateContinuousDataSet0.060.000.06
sortGeneTrajectories15.23 0.0015.24
sub-sub-LineagePulseObject-character-missing-method20.93 0.0620.98
testDropout16.87 0.0116.89
writeReport21.50 0.0021.52