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This page was generated on 2023-02-04 11:06:13 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 merida1


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 965/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.29.0  (landing page)
Stefano de Pretis
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: master
git_last_commit: 5409025
git_last_commit_date: 2022-11-01 11:11:51 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: INSPEcT
Version: 1.29.0
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_1.29.0.tar.gz
StartedAt: 2023-02-04 02:33:45 -0500 (Sat, 04 Feb 2023)
EndedAt: 2023-02-04 03:08:29 -0500 (Sat, 04 Feb 2023)
EllapsedTime: 2084.2 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_1.29.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.29.0’
* 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                  205.341  0.667 282.246
quantifyExpressionsFromBAMs      67.191  4.883  97.606
rocThresholds                    71.592  0.264  95.226
makeSimModel                     70.897  0.244  93.563
rocCurve                         70.598  0.258  97.410
INSPEcT_diffsteady-class         66.800  0.475  95.348
compareSteady                    60.637  0.203  85.836
plotMA                           60.492  0.171  79.901
modelRates                       39.820  0.115  52.387
newINSPEcT                       39.462  0.108  52.126
quantifyExpressionsFromTrCounts  34.402  0.113  46.458
processingDelay                  33.198  0.093  43.401
makeOscillatorySimModel          16.825  0.086  24.529
compareSteadyNoNascent           13.832  0.054  19.082
inspectFromPCR                    8.562  0.039  11.799
* 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-3.17-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.



Installation output

INSPEcT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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-method0.3730.0150.571
Extract0.7780.0331.185
INSPEcT_diffsteady-class66.800 0.47595.348
calculateRatePvals0.4750.0140.723
chisqmodel0.3750.0150.547
chisqtest0.3700.0130.534
combine0.7540.0071.076
compareSteady60.637 0.20385.836
compareSteadyNoNascent13.832 0.05419.082
convergence0.3660.0070.524
geneClass0.4720.0070.677
inHeatmap0.4410.0130.606
inspectFromPCR 8.562 0.03911.799
labeledSF0.3740.0150.542
logLik0.3730.0140.547
makeModelRates0.4720.0130.679
makeOscillatorySimModel16.825 0.08624.529
makeSimDataset205.341 0.667282.246
makeSimModel70.897 0.24493.563
modelRates39.820 0.11552.387
modelRatesNF3.2830.0434.340
modelSelection0.3800.0140.516
modelingParams0.3730.0130.515
nGenes0.3730.0120.508
nTpts0.3770.0100.506
newINSPEcT39.462 0.10852.126
plotGene0.4440.0050.608
plotMA60.492 0.17179.901
processingDelay33.198 0.09343.401
quantifyExpressionsFromBAMs67.191 4.88397.606
quantifyExpressionsFromTrCounts34.402 0.11346.458
ratePvals0.3720.0040.508
ratesFirstGuess0.3680.0050.523
ratesFirstGuessVar0.3660.0050.499
removeModel0.5790.0040.803
rocCurve70.598 0.25897.410
rocThresholds71.592 0.26495.226
split0.5640.0040.701
tpts0.3700.0030.456
viewConfidenceIntervals0.3750.0050.465
viewModelRates0.3670.0040.471