Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:11 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 INSPEcT on machv2


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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
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 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.24.0.tar.gz
StartedAt: 2022-04-12 14:29:39 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 14:52:13 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 1354.1 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/INSPEcT.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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  7.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    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                  167.976  0.437 168.531
quantifyExpressionsFromBAMs      63.656 13.218  77.449
INSPEcT_diffsteady-class         67.364  0.566  68.015
compareSteady                    65.207  0.271  65.555
plotMA                           62.031  0.237  62.326
rocThresholds                    60.267  0.163  60.510
rocCurve                         60.011  0.167  60.240
makeSimModel                     56.875  0.145  57.078
quantifyExpressionsFromTrCounts  39.614  0.075  39.736
newINSPEcT                       36.979  0.198  37.210
processingDelay                  36.742  0.121  37.325
modelRates                       33.266  0.134  33.428
compareSteadyNoNascent           16.032  0.043  16.090
makeOscillatorySimModel          14.067  0.057  14.138
inspectFromPCR                    6.874  0.039   6.919
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.



Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-method0.2970.0130.312
Extract0.7850.0090.794
INSPEcT_diffsteady-class67.364 0.56668.015
calculateRatePvals0.4510.0140.466
chisqmodel0.2690.0050.274
chisqtest0.3120.0130.325
combine0.6460.0100.656
compareSteady65.207 0.27165.555
compareSteadyNoNascent16.032 0.04316.090
convergence0.3070.0110.320
geneClass0.4360.0110.449
inHeatmap0.3710.0150.389
inspectFromPCR6.8740.0396.919
labeledSF0.3370.0060.344
logLik0.3240.0130.336
makeModelRates0.4270.0130.442
makeOscillatorySimModel14.067 0.05714.138
makeSimDataset167.976 0.437168.531
makeSimModel56.875 0.14557.078
modelRates33.266 0.13433.428
modelRatesNF2.5360.0502.588
modelSelection0.3140.0090.324
modelingParams0.3310.0030.334
nGenes0.2970.0030.299
nTpts0.3090.0060.316
newINSPEcT36.979 0.19837.210
plotGene0.3070.0080.316
plotMA62.031 0.23762.326
processingDelay36.742 0.12137.325
quantifyExpressionsFromBAMs63.65613.21877.449
quantifyExpressionsFromTrCounts39.614 0.07539.736
ratePvals0.2860.0030.289
ratesFirstGuess0.2980.0070.306
ratesFirstGuessVar0.2160.0040.220
removeModel0.5090.0040.512
rocCurve60.011 0.16760.240
rocThresholds60.267 0.16360.510
split0.5030.0030.508
tpts0.3360.0030.339
viewConfidenceIntervals0.3110.0100.321
viewModelRates0.3340.0060.341