Package: LineagePulse

Version: 1.2.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LineagePulse_1.2.1.tar.gz

StartedAt: 2019-04-13 03:23:35 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:34:51 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 676.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: LineagePulse.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LineagePulse_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/LineagePulse.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-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 or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     38.32   0.03   38.34
getFitsDispersion                                   12.73   0.03   12.77
accessors                                           12.56   0.17   12.73
cash-LineagePulseObject-method                      12.66   0.02   12.67
sub-sub-LineagePulseObject-character-missing-method 12.67   0.00   12.67
getPostDrop                                         12.61   0.00   12.61
writeReport                                         12.53   0.00   12.53
getFitsDropout                                      12.20   0.01   12.22
names-LineagePulseObject-method                     12.14   0.00   12.14
getNormData                                         12.11   0.02   12.12
getFitsMean                                         11.77   0.02   11.78
testDropout                                         10.17   0.00   10.17
plotGene                                             9.79   0.00    9.80
sortGeneTrajectories                                 9.78   0.00    9.78
runLineagePulse                                      9.74   0.00    9.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     41.97   0.01   41.99
getFitsDropout                                      17.16   0.02   17.17
getFitsDispersion                                   16.28   0.05   16.33
getFitsMean                                         16.31   0.01   16.33
names-LineagePulseObject-method                     15.38   0.02   15.39
cash-LineagePulseObject-method                      15.36   0.02   15.37
getNormData                                         15.05   0.00   15.04
getPostDrop                                         14.54   0.00   14.55
accessors                                           14.46   0.06   14.51
writeReport                                         14.25   0.00   14.25
sub-sub-LineagePulseObject-character-missing-method 14.22   0.00   14.22
testDropout                                         11.25   0.00   11.25
plotGene                                            11.22   0.00   11.22
sortGeneTrajectories                                11.14   0.02   11.15
runLineagePulse                                     10.89   0.01   10.91
* 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-3.8-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/LineagePulse_1.2.1.tar.gz && rm -rf LineagePulse.buildbin-libdir && mkdir LineagePulse.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LineagePulse.buildbin-libdir LineagePulse_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL LineagePulse_1.2.1.zip && rm LineagePulse_1.2.1.tar.gz LineagePulse_1.2.1.zip
###
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install for i386

* installing *source* package 'LineagePulse' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'LineagePulse' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LineagePulse' as LineagePulse_1.2.1.zip
* DONE (LineagePulse)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'LineagePulse' successfully unpacked and MD5 sums checked
In R CMD INSTALL