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This page was generated on 2024-05-26 11:35:19 -0400 (Sun, 26 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4665
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4427
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

Package 1008/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.35.0  (landing page)
Stefano de Pretis
Snapshot Date: 2024-05-24 14:05:03 -0400 (Fri, 24 May 2024)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: devel
git_last_commit: 08b5f2f
git_last_commit_date: 2024-04-30 10:44:32 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for INSPEcT on merida1


To the developers/maintainers of the INSPEcT package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: INSPEcT
Version: 1.35.0
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_1.35.0.tar.gz
StartedAt: 2024-05-25 09:02:30 -0400 (Sat, 25 May 2024)
EndedAt: 2024-05-25 09:38:11 -0400 (Sat, 25 May 2024)
EllapsedTime: 2141.6 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_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/INSPEcT.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.35.0’
* 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 code 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                  238.668  1.352 281.075
modelRates                      105.575  0.563 125.608
makeSimModel                     82.619  0.536  96.160
rocCurve                         81.732  0.539  92.699
rocThresholds                    80.577  0.562  92.389
quantifyExpressionsFromBAMs      72.955  6.000  89.021
INSPEcT_diffsteady-class         74.062  0.885  90.228
plotMA                           67.581  0.406  76.866
compareSteady                    66.652  0.394  79.762
newINSPEcT                       42.439  0.274  50.366
quantifyExpressionsFromTrCounts  36.879  0.276  43.329
processingDelay                  35.890  0.208  40.066
makeOscillatorySimModel          19.994  0.212  23.518
inspectFromPCR                   18.466  0.134  21.528
compareSteadyNoNascent           14.406  0.100  17.221
modelRatesNF                     11.824  0.257  14.418
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-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/4.4-x86_64/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-method0.3580.0240.446
Extract0.8390.0501.066
INSPEcT_diffsteady-class74.062 0.88590.228
calculateRatePvals0.4750.0200.614
chisqmodel0.3580.0180.461
chisqtest0.3550.0170.466
combine0.7850.0100.976
compareSteady66.652 0.39479.762
compareSteadyNoNascent14.406 0.10017.221
convergence0.3560.0200.454
geneClass0.4850.0210.592
inHeatmap0.4350.0180.543
inspectFromPCR18.466 0.13421.528
labeledSF0.3570.0200.455
logLik0.3570.0210.438
makeModelRates0.4750.0240.566
makeOscillatorySimModel19.994 0.21223.518
makeSimDataset238.668 1.352281.075
makeSimModel82.619 0.53696.160
modelRates105.575 0.563125.608
modelRatesNF11.824 0.25714.418
modelSelection0.3520.0210.417
modelingParams0.3490.0090.392
nGenes0.3540.0160.418
nTpts0.3550.0150.417
newINSPEcT42.439 0.27450.366
plotGene0.4440.0090.555
plotMA67.581 0.40676.866
processingDelay35.890 0.20840.066
quantifyExpressionsFromBAMs72.955 6.00089.021
quantifyExpressionsFromTrCounts36.879 0.27643.329
ratePvals0.3540.0060.397
ratesFirstGuess0.3550.0120.414
ratesFirstGuessVar0.3570.0130.427
removeModel0.6050.0070.677
rocCurve81.732 0.53992.699
rocThresholds80.577 0.56292.389
split0.5860.0070.661
tpts0.3480.0070.403
viewConfidenceIntervals0.3560.0150.411
viewModelRates0.3530.0090.398