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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).

CHECK results for LineagePulse on tokay2

To the developers/maintainers of the LineagePulse package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LineagePulse.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 987/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LineagePulse 1.12.0  (landing page)
David S Fischer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/LineagePulse
git_branch: RELEASE_3_13
git_last_commit: 6b86f9a
git_last_commit_date: 2021-05-19 12:32:15 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: LineagePulse
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings LineagePulse_1.12.0.tar.gz
StartedAt: 2021-10-15 01:08:21 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:21:15 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 773.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: LineagePulse.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings LineagePulse_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/LineagePulse.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.12.0'
* 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-3.13-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                                     45.88   0.00   45.88
sortGeneTrajectories                                16.49   0.04   16.52
getFitsDropout                                      16.33   0.00   16.33
cash-LineagePulseObject-method                      16.24   0.00   16.23
accessors                                           15.89   0.22   16.11
names-LineagePulseObject-method                     16.09   0.00   16.09
testDropout                                         15.94   0.00   15.94
getFitsDispersion                                   15.48   0.08   15.56
writeReport                                         15.20   0.02   15.22
sub-sub-LineagePulseObject-character-missing-method 15.14   0.01   15.15
getPostDrop                                         15.08   0.00   15.08
getNormData                                         14.86   0.01   14.87
runLineagePulse                                     14.75   0.00   14.75
getFitsMean                                         14.34   0.00   14.35
plotGene                                            13.81   0.00   13.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     48.43   0.11   48.53
plotGene                                            19.81   0.00   19.81
sortGeneTrajectories                                19.30   0.04   19.34
accessors                                           18.66   0.00   18.65
sub-sub-LineagePulseObject-character-missing-method 18.50   0.02   18.52
getNormData                                         17.75   0.00   17.75
runLineagePulse                                     17.65   0.00   17.66
names-LineagePulseObject-method                     17.56   0.00   17.56
cash-LineagePulseObject-method                      17.44   0.01   17.45
writeReport                                         17.28   0.00   17.28
testDropout                                         17.04   0.00   17.04
getFitsMean                                         16.80   0.00   16.80
getFitsDropout                                      16.74   0.00   16.73
getFitsDispersion                                   16.68   0.00   16.69
getPostDrop                                         16.37   0.00   16.37
* 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-3.13-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.

Installation output

LineagePulse.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/LineagePulse_1.12.0.tar.gz && rm -rf LineagePulse.buildbin-libdir && mkdir LineagePulse.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LineagePulse.buildbin-libdir LineagePulse_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL LineagePulse_1.12.0.zip && rm LineagePulse_1.12.0.tar.gz LineagePulse_1.12.0.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
  3 73196    3  2488    0     0  30193      0  0:00:02 --:--:--  0:00:02 30341
100 73196  100 73196    0     0   350k      0 --:--:-- --:--:-- --:--:--  350k

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_1.12.0.zip
* DONE (LineagePulse)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'LineagePulse' successfully unpacked and MD5 sums checked

Tests output

Example timings

LineagePulse.Rcheck/examples_i386/LineagePulse-Ex.timings

nameusersystemelapsed
accessors15.89 0.2216.11
cash-LineagePulseObject-method16.24 0.0016.23
getFitsDispersion15.48 0.0815.56
getFitsDropout16.33 0.0016.33
getFitsMean14.34 0.0014.35
getNormData14.86 0.0114.87
getPostDrop15.08 0.0015.08
names-LineagePulseObject-method16.09 0.0016.09
plotCellDensity45.88 0.0045.88
plotGene13.81 0.0013.81
runLineagePulse14.75 0.0014.75
simulateContinuousDataSet0.030.000.03
sortGeneTrajectories16.49 0.0416.52
sub-sub-LineagePulseObject-character-missing-method15.14 0.0115.15
testDropout15.94 0.0015.94
writeReport15.20 0.0215.22

LineagePulse.Rcheck/examples_x64/LineagePulse-Ex.timings

nameusersystemelapsed
accessors18.66 0.0018.65
cash-LineagePulseObject-method17.44 0.0117.45
getFitsDispersion16.68 0.0016.69
getFitsDropout16.74 0.0016.73
getFitsMean16.8 0.016.8
getNormData17.75 0.0017.75
getPostDrop16.37 0.0016.37
names-LineagePulseObject-method17.56 0.0017.56
plotCellDensity48.43 0.1148.53
plotGene19.81 0.0019.81
runLineagePulse17.65 0.0017.66
simulateContinuousDataSet0.020.000.02
sortGeneTrajectories19.30 0.0419.34
sub-sub-LineagePulseObject-character-missing-method18.50 0.0218.52
testDropout17.04 0.0017.04
writeReport17.28 0.0017.28