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This page was generated on 2022-01-21 13:06:33 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 999/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LineagePulse 1.14.0  (landing page)
David S Fischer
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/LineagePulse
git_branch: RELEASE_3_14
git_last_commit: 23b2bf4
git_last_commit_date: 2021-10-26 12:40:27 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings LineagePulse_1.14.0.tar.gz
StartedAt: 2022-01-20 22:07:30 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 22:19:23 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 712.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: LineagePulse.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings LineagePulse_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/LineagePulse.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.14.0'
* 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-3.14-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                                     39.57   0.09   39.65
accessors                                           15.36   0.19   15.54
cash-LineagePulseObject-method                      15.39   0.00   15.39
names-LineagePulseObject-method                     15.08   0.00   15.08
getFitsDropout                                      14.86   0.01   14.89
writeReport                                         14.73   0.01   14.75
getFitsDispersion                                   14.33   0.03   14.36
getNormData                                         14.03   0.00   14.03
getPostDrop                                         14.02   0.00   14.01
sub-sub-LineagePulseObject-character-missing-method 14.00   0.00   14.00
getFitsMean                                         13.82   0.02   13.85
sortGeneTrajectories                                12.29   0.00   12.28
plotGene                                            11.82   0.00   11.83
testDropout                                         11.75   0.03   11.78
runLineagePulse                                     10.83   0.02   10.84
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
plotCellDensity                                     42.05   0.03   42.08
writeReport                                         17.59   0.00   17.59
sub-sub-LineagePulseObject-character-missing-method 17.37   0.00   17.38
names-LineagePulseObject-method                     17.03   0.00   17.03
accessors                                           16.89   0.01   16.90
getFitsDispersion                                   16.63   0.00   16.63
cash-LineagePulseObject-method                      16.55   0.00   16.55
getFitsMean                                         16.53   0.02   16.56
getPostDrop                                         16.22   0.02   16.23
getNormData                                         16.17   0.01   16.19
getFitsDropout                                      16.17   0.00   16.19
testDropout                                         13.58   0.00   13.58
sortGeneTrajectories                                13.46   0.02   13.47
runLineagePulse                                     12.34   0.00   12.34
plotGene                                            12.22   0.00   12.22
* 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-3.14-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.



Installation output

LineagePulse.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/LineagePulse_1.14.0.tar.gz && rm -rf LineagePulse.buildbin-libdir && mkdir LineagePulse.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LineagePulse.buildbin-libdir LineagePulse_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL LineagePulse_1.14.0.zip && rm LineagePulse_1.14.0.tar.gz LineagePulse_1.14.0.zip
###
##############################################################################
##############################################################################


  % 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 75738  100 75738    0     0   487k      0 --:--:-- --:--:-- --:--:--  489k

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_1.14.0.zip
* DONE (LineagePulse)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'LineagePulse' successfully unpacked and MD5 sums checked

Tests output


Example timings

LineagePulse.Rcheck/examples_i386/LineagePulse-Ex.timings

nameusersystemelapsed
accessors15.36 0.1915.54
cash-LineagePulseObject-method15.39 0.0015.39
getFitsDispersion14.33 0.0314.36
getFitsDropout14.86 0.0114.89
getFitsMean13.82 0.0213.85
getNormData14.03 0.0014.03
getPostDrop14.02 0.0014.01
names-LineagePulseObject-method15.08 0.0015.08
plotCellDensity39.57 0.0939.65
plotGene11.82 0.0011.83
runLineagePulse10.83 0.0210.84
simulateContinuousDataSet0.010.000.02
sortGeneTrajectories12.29 0.0012.28
sub-sub-LineagePulseObject-character-missing-method14 014
testDropout11.75 0.0311.78
writeReport14.73 0.0114.75

LineagePulse.Rcheck/examples_x64/LineagePulse-Ex.timings

nameusersystemelapsed
accessors16.89 0.0116.90
cash-LineagePulseObject-method16.55 0.0016.55
getFitsDispersion16.63 0.0016.63
getFitsDropout16.17 0.0016.19
getFitsMean16.53 0.0216.56
getNormData16.17 0.0116.19
getPostDrop16.22 0.0216.23
names-LineagePulseObject-method17.03 0.0017.03
plotCellDensity42.05 0.0342.08
plotGene12.22 0.0012.22
runLineagePulse12.34 0.0012.34
simulateContinuousDataSet0.030.000.03
sortGeneTrajectories13.46 0.0213.47
sub-sub-LineagePulseObject-character-missing-method17.37 0.0017.38
testDropout13.58 0.0013.58
writeReport17.59 0.0017.59