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This page was generated on 2021-12-06 13:05:01 -0500 (Mon, 06 Dec 2021).

CHECK results for INSPEcT on nebbiolo2

To the developers/maintainers of the INSPEcT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/INSPEcT.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 936/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.24.0  (landing page)
Stefano de Pretis
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_14
git_last_commit: ed551fb
git_last_commit_date: 2021-10-26 12:21:19 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: INSPEcT
Version: 1.24.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings INSPEcT_1.24.0.tar.gz
StartedAt: 2021-12-05 08:21:39 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 08:33:32 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 713.2 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings INSPEcT_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/INSPEcT.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘INSPEcT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  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
* 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’
plotSingleRNADynamic: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new
Consider adding
  importFrom("graphics", "lines", "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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
makeSimDataset                  72.180  0.740  72.921
quantifyExpressionsFromBAMs     34.930  3.459  38.730
modelRates                      35.504  0.392  35.897
INSPEcT_diffsteady-class        32.317  0.500  32.831
compareSteady                   29.749  0.308  30.057
plotMA                          29.310  0.123  29.435
rocCurve                        24.586  0.016  24.604
rocThresholds                   24.256  0.024  24.281
makeSimModel                    23.556  0.212  23.769
quantifyExpressionsFromTrCounts 21.945  0.024  21.970
newINSPEcT                      17.851  0.848  18.700
processingDelay                 18.616  0.024  18.640
compareSteadyNoNascent           7.944  0.083   8.028
inspectFromPCR                   5.972  0.096   6.068
makeOscillatorySimModel          5.698  0.076   5.775
modelRatesNF                     5.077  0.103   5.182
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.



Installation output

INSPEcT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘INSPEcT’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (INSPEcT)

Tests output


Example timings

INSPEcT.Rcheck/INSPEcT-Ex.timings

nameusersystemelapsed
AIC-INSPEcT-method0.1990.0080.207
Extract0.4340.0240.458
INSPEcT_diffsteady-class32.317 0.50032.831
calculateRatePvals0.2120.0080.220
chisqmodel0.1740.0000.174
chisqtest0.1760.0000.176
combine0.3370.0040.341
compareSteady29.749 0.30830.057
compareSteadyNoNascent7.9440.0838.028
convergence0.1690.0090.177
geneClass0.2090.0040.213
inHeatmap0.2070.0000.207
inspectFromPCR5.9720.0966.068
labeledSF0.1800.0030.184
logLik0.1770.0050.181
makeModelRates0.2040.0080.211
makeOscillatorySimModel5.6980.0765.775
makeSimDataset72.180 0.74072.921
makeSimModel23.556 0.21223.769
modelRates35.504 0.39235.897
modelRatesNF5.0770.1035.182
modelSelection0.1760.0000.176
modelingParams0.1760.0000.176
nGenes0.1670.0080.175
nTpts0.1720.0000.172
newINSPEcT17.851 0.84818.700
plotGene0.2070.0240.231
plotMA29.310 0.12329.435
processingDelay18.616 0.02418.640
quantifyExpressionsFromBAMs34.930 3.45938.730
quantifyExpressionsFromTrCounts21.945 0.02421.970
ratePvals0.1780.0000.178
ratesFirstGuess0.1750.0020.177
ratesFirstGuessVar0.1760.0010.178
removeModel0.2660.0000.266
rocCurve24.586 0.01624.604
rocThresholds24.256 0.02424.281
split0.2570.0000.257
tpts0.1720.0000.172
viewConfidenceIntervals0.1750.0000.175
viewModelRates0.1730.0000.173