Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:07:49 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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? 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: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 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 -0500 (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: 2022-01-23 14:14:15 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 14:36:41 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 1345.5 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
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/INSPEcT.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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  7.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    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                  170.127  0.442 170.700
quantifyExpressionsFromBAMs      62.594 11.486  74.643
INSPEcT_diffsteady-class         67.570  0.538  68.226
compareSteady                    65.096  0.275  65.452
plotMA                           63.344  0.213  64.149
rocThresholds                    60.212  0.213  60.551
rocCurve                         59.631  0.183  59.874
makeSimModel                     54.491  0.158  54.701
quantifyExpressionsFromTrCounts  40.289  0.074  40.403
processingDelay                  39.040  0.107  39.182
newINSPEcT                       36.376  0.181  36.590
modelRates                       31.950  0.123  32.103
compareSteadyNoNascent           16.728  0.035  16.772
makeOscillatorySimModel          14.237  0.062  14.315
inspectFromPCR                    6.528  0.045   6.581
* 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-method0.3520.0090.363
Extract0.7860.0160.802
INSPEcT_diffsteady-class67.570 0.53868.226
calculateRatePvals0.4340.0030.437
chisqmodel0.3510.0100.361
chisqtest0.3450.0060.351
combine0.6330.0120.645
compareSteady65.096 0.27565.452
compareSteadyNoNascent16.728 0.03516.772
convergence0.3170.0100.327
geneClass0.4410.0070.448
inHeatmap0.4190.0140.434
inspectFromPCR6.5280.0456.581
labeledSF0.3020.0110.313
logLik0.3050.0110.317
makeModelRates0.3610.0120.374
makeOscillatorySimModel14.237 0.06214.315
makeSimDataset170.127 0.442170.700
makeSimModel54.491 0.15854.701
modelRates31.950 0.12332.103
modelRatesNF2.7170.0522.771
modelSelection0.2740.0090.283
modelingParams0.3420.0060.348
nGenes0.3900.0150.406
nTpts0.2990.0100.309
newINSPEcT36.376 0.18136.590
plotGene0.2700.0040.274
plotMA63.344 0.21364.149
processingDelay39.040 0.10739.182
quantifyExpressionsFromBAMs62.59411.48674.643
quantifyExpressionsFromTrCounts40.289 0.07440.403
ratePvals0.3240.0050.330
ratesFirstGuess0.2700.0060.275
ratesFirstGuessVar0.3150.0080.323
removeModel0.5270.0050.532
rocCurve59.631 0.18359.874
rocThresholds60.212 0.21360.551
split0.4900.0050.496
tpts0.3060.0060.313
viewConfidenceIntervals0.3000.0130.315
viewModelRates0.2890.0070.298