Back to Multiple platform build/check report for BioC 3.15
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2022-06-24 12:07:37 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 961/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.26.0  (landing page)
Stefano de Pretis
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_15
git_last_commit: 8ba12ec
git_last_commit_date: 2022-04-26 11:26:03 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: INSPEcT
Version: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2022-06-24 04:08:46 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:35:17 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 1590.5 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/INSPEcT.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.26.0’
* 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                  204.977  0.544 207.938
quantifyExpressionsFromBAMs      65.901  6.821  76.558
rocCurve                         70.311  0.281  74.707
rocThresholds                    70.050  0.236  74.825
makeSimModel                     69.674  0.212  70.861
INSPEcT_diffsteady-class         65.379  0.464  67.306
compareSteady                    63.086  0.178  64.456
plotMA                           62.910  0.170  66.540
modelRates                       39.669  0.117  40.857
newINSPEcT                       39.095  0.095  40.003
quantifyExpressionsFromTrCounts  34.903  0.099  36.190
processingDelay                  33.082  0.090  34.838
makeOscillatorySimModel          17.084  0.084  17.627
compareSteadyNoNascent           13.985  0.046  14.666
inspectFromPCR                    8.764  0.044   9.264
* 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-3.15-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/4.2/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-method0.3740.0130.406
Extract0.7590.0160.805
INSPEcT_diffsteady-class65.379 0.46467.306
calculateRatePvals0.4820.0120.498
chisqmodel0.3760.0050.384
chisqtest0.3850.0140.400
combine0.7510.0120.769
compareSteady63.086 0.17864.456
compareSteadyNoNascent13.985 0.04614.666
convergence0.3830.0110.422
geneClass0.4790.0080.507
inHeatmap0.4310.0120.447
inspectFromPCR8.7640.0449.264
labeledSF0.3770.0120.407
logLik0.3800.0130.409
makeModelRates0.4790.0070.512
makeOscillatorySimModel17.084 0.08417.627
makeSimDataset204.977 0.544207.938
makeSimModel69.674 0.21270.861
modelRates39.669 0.11740.857
modelRatesNF3.2490.0433.328
modelSelection0.3770.0040.387
modelingParams0.3700.0060.381
nGenes0.3740.0100.387
nTpts0.3760.0070.385
newINSPEcT39.095 0.09540.003
plotGene0.4550.0150.473
plotMA62.91 0.1766.54
processingDelay33.082 0.09034.838
quantifyExpressionsFromBAMs65.901 6.82176.558
quantifyExpressionsFromTrCounts34.903 0.09936.190
ratePvals0.3710.0040.404
ratesFirstGuess0.3730.0050.384
ratesFirstGuessVar0.3660.0050.422
removeModel0.5850.0040.606
rocCurve70.311 0.28174.707
rocThresholds70.050 0.23674.825
split0.5670.0040.616
tpts0.3620.0030.377
viewConfidenceIntervals0.3720.0050.385
viewModelRates0.3720.0040.403