Package: LineagePulse

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings LineagePulse_1.4.0.tar.gz

StartedAt: 2019-10-16 04:48:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:00:29 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 748.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: LineagePulse.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings LineagePulse_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/LineagePulse.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.4.0'
* 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 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-3.9-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
* 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 : : 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     43.87   0.02   43.89
accessors                                           17.33   0.32   17.66
getFitsDispersion                                   16.06   0.06   16.13
writeReport                                         15.69   0.02   15.71
getFitsMean                                         15.55   0.11   15.66
sub-sub-LineagePulseObject-character-missing-method 15.64   0.00   15.64
getNormData                                         15.52   0.03   15.54
getPostDrop                                         15.29   0.05   15.35
getFitsDropout                                      14.89   0.06   14.95
names-LineagePulseObject-method                     14.88   0.01   14.89
cash-LineagePulseObject-method                      14.61   0.07   14.67
sortGeneTrajectories                                13.27   0.00   13.27
testDropout                                         12.46   0.01   12.48
runLineagePulse                                     11.89   0.00   11.89
plotGene                                            11.33   0.00   11.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     40.99   0.01   41.00
getFitsDropout                                      20.94   0.00   21.05
accessors                                           20.75   0.01   20.77
sub-sub-LineagePulseObject-character-missing-method 20.05   0.00   20.05
getFitsMean                                         19.45   0.04   19.48
getNormData                                         19.00   0.00   19.00
getPostDrop                                         18.27   0.00   18.27
getFitsDispersion                                   17.36   0.00   17.37
writeReport                                         16.92   0.00   16.92
cash-LineagePulseObject-method                      15.95   0.00   15.95
names-LineagePulseObject-method                     15.65   0.00   15.68
plotGene                                            15.43   0.00   15.44
sortGeneTrajectories                                14.61   0.02   14.62
testDropout                                         13.86   0.00   13.86
runLineagePulse                                     12.96   0.00   12.95
* 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-3.9-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/LineagePulse_1.4.0.tar.gz && rm -rf LineagePulse.buildbin-libdir && mkdir LineagePulse.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LineagePulse.buildbin-libdir LineagePulse_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL LineagePulse_1.4.0.zip && rm LineagePulse_1.4.0.tar.gz LineagePulse_1.4.0.zip
###
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100 74618  100 74618    0     0  1227k      0 --:--:-- --:--:-- --:--:-- 1401k

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_1.4.0.zip
* DONE (LineagePulse)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'LineagePulse' successfully unpacked and MD5 sums checked