Back to Multiple platform build/check report for BioC 3.11
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for INSPEcT on tokay2

This page was generated on 2020-10-17 11:56:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE INSPEcT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 879/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.18.1
Stefano de Pretis
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/INSPEcT
Branch: RELEASE_3_11
Last Commit: 07cd1ed
Last Changed Date: 2020-10-05 08:08:00 -0400 (Mon, 05 Oct 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: INSPEcT
Version: 1.18.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:INSPEcT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings INSPEcT_1.18.1.tar.gz
StartedAt: 2020-10-17 05:13:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:30:59 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 1029.5 seconds
RetCode: 0
Status:  OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:INSPEcT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings INSPEcT_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/INSPEcT.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 'INSPEcT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'INSPEcT' version '1.18.1'
* 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 'INSPEcT' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.8Mb
* 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
output_pars: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  plot.new
Consider adding
  importFrom("graphics", "plot.new")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
makeSimModel                    27.83   0.09   27.95
quantifyExpressionsFromTrCounts 22.24   0.02   22.25
processingDelay                 17.87   0.11   18.00
newINSPEcT                      17.73   0.08   17.81
compareSteadyNoNascent           6.99   0.75    7.73
makeOscillatorySimModel          6.89   0.14    7.23
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
makeSimModel                    35.86   0.06   35.93
quantifyExpressionsFromTrCounts 23.09   0.00   23.14
processingDelay                 19.28   0.00   19.28
newINSPEcT                      17.59   0.03   17.62
makeOscillatorySimModel         11.89   0.04   12.09
compareSteadyNoNascent           9.20   0.08    9.28
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/INSPEcT.Rcheck/00check.log'
for details.



Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/INSPEcT_1.18.1.tar.gz && rm -rf INSPEcT.buildbin-libdir && mkdir INSPEcT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=INSPEcT.buildbin-libdir INSPEcT_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL INSPEcT_1.18.1.zip && rm INSPEcT_1.18.1.tar.gz INSPEcT_1.18.1.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 5874k  100 5874k    0     0  45.7M      0 --:--:-- --:--:-- --:--:-- 47.8M

install for i386

* installing *source* package 'INSPEcT' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'INSPEcT'
    finding HTML links ... done
    AIC-INSPEcT-method                      html  
    Extract                                 html  
    INSPEcT-class                           html  
    finding level-2 HTML links ... done

    INSPEcT-shinyApps                       html  
    INSPEcT                                 html  
    INSPEcT_diffsteady-class                html  
    INSPEcT_model-class                     html  
    INSPEcT_steadyNoNascent-class           html  
    PTratio                                 html  
    PTreg                                   html  
    allcounts                               html  
    calculateRatePvals                      html  
    chisqmodel                              html  
    chisqtest                               html  
    combine                                 html  
    compareSteady                           html  
    compareSteadyNoNascent                  html  
    computeConfidenceIntervals              html  
    convergence                             html  
    correlationPlot                         html  
    dim-INSPEcT-method                      html  
    featureNames-INSPEcT-method             html  
    featureWidths                           html  
    geneClass                               html  
    inHeatmap                               html  
    inspectFromBAM                          html  
    inspectFromPCR                          html  
    labeledSF                               html  
    libsizes                                html  
    logLik                                  html  
    makeModelRates                          html  
    makeOscillatorySimModel                 html  
    makeSimDataset                          html  
    makeSimModel                            html  
    mature                                  html  
    matureVar                               html  
    modelRates                              html  
    modelRatesNF                            html  
    modelSelection                          html  
    modelingParams                          html  
    nGenes                                  html  
    nTpts                                   html  
    newINSPEcT                              html  
    plotGene                                html  
    plotMA                                  html  
    plotPMgene                              html  
    plotPMtrend                             html  
    premature                               html  
    prematureVar                            html  
    processingDelay                         html  
    quantifyExpressionsFromBAMs             html  
    quantifyExpressionsFromBWs              html  
    quantifyExpressionsFromTrAbundance      html  
    quantifyExpressionsFromTrCounts         html  
    ratePvals                               html  
    ratesFirstGuess                         html  
    ratesFirstGuessVar                      html  
    removeModel                             html  
    rocCurve                                html  
    rocThresholds                           html  
    setConfidenceIntervals                  html  
    simData3rep_Nascent                     html  
    simData3rep_NoNascent                   html  
    simData4rep_Nascent                     html  
    simData4rep_NoNascent                   html  
    split                                   html  
    tpts                                    html  
    viewConfidenceIntervals                 html  
    viewModelRates                          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 'INSPEcT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'INSPEcT' as INSPEcT_1.18.1.zip
* DONE (INSPEcT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'INSPEcT' successfully unpacked and MD5 sums checked

Tests output


Example timings

INSPEcT.Rcheck/examples_i386/INSPEcT-Ex.timings

nameusersystemelapsed
AIC-INSPEcT-method0.490.000.53
Extract0.540.000.55
INSPEcT_diffsteady-class000
calculateRatePvals0.360.000.36
chisqmodel0.270.020.29
chisqtest0.280.010.29
combine1.180.001.19
compareSteady000
compareSteadyNoNascent6.990.757.73
convergence0.260.000.27
geneClass0.300.010.31
inHeatmap0.420.020.44
inspectFromPCR000
labeledSF0.450.020.47
logLik0.490.010.50
makeModelRates0.420.020.44
makeOscillatorySimModel6.890.147.23
makeSimDataset000
makeSimModel27.83 0.0927.95
modelRates000
modelRatesNF000
modelSelection0.250.000.25
modelingParams0.220.030.25
nGenes0.250.000.25
nTpts0.230.000.24
newINSPEcT17.73 0.0817.81
plotGene0.430.000.42
plotMA000
processingDelay17.87 0.1118.00
quantifyExpressionsFromBAMs000
quantifyExpressionsFromTrCounts22.24 0.0222.25
ratePvals0.400.000.41
ratesFirstGuess0.420.000.42
ratesFirstGuessVar0.440.000.43
removeModel0.510.030.55
rocCurve000
rocThresholds0.020.000.01
split0.580.000.58
tpts0.400.020.42
viewConfidenceIntervals0.250.000.25
viewModelRates0.270.000.27

INSPEcT.Rcheck/examples_x64/INSPEcT-Ex.timings

nameusersystemelapsed
AIC-INSPEcT-method0.190.020.20
Extract0.500.010.52
INSPEcT_diffsteady-class000
calculateRatePvals0.370.000.37
chisqmodel0.380.020.39
chisqtest0.370.000.39
combine0.600.030.63
compareSteady000
compareSteadyNoNascent9.200.089.28
convergence0.20.00.2
geneClass0.250.010.27
inHeatmap0.250.020.27
inspectFromPCR000
labeledSF0.360.000.35
logLik0.350.020.36
makeModelRates0.400.000.41
makeOscillatorySimModel11.89 0.0412.09
makeSimDataset000
makeSimModel35.86 0.0635.93
modelRates000
modelRatesNF0.020.000.01
modelSelection0.220.000.22
modelingParams0.180.020.20
nGenes0.210.000.21
nTpts0.170.030.20
newINSPEcT17.59 0.0317.62
plotGene0.250.000.25
plotMA000
processingDelay19.28 0.0019.28
quantifyExpressionsFromBAMs0.020.000.02
quantifyExpressionsFromTrCounts23.09 0.0023.14
ratePvals0.210.000.20
ratesFirstGuess0.180.010.20
ratesFirstGuessVar0.210.020.22
removeModel0.280.000.28
rocCurve000
rocThresholds000
split0.300.020.32
tpts0.180.010.20
viewConfidenceIntervals0.210.000.20
viewModelRates0.250.000.25