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This page was generated on 2023-03-31 11:06:46 -0400 (Fri, 31 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4498
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4278
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4306
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 lconway


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 976/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.28.0  (landing page)
Stefano de Pretis
Snapshot Date: 2023-03-29 14:00:04 -0400 (Wed, 29 Mar 2023)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_16
git_last_commit: aff3971
git_last_commit_date: 2022-11-01 11:11:51 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: INSPEcT
Version: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2023-03-29 20:46:07 -0400 (Wed, 29 Mar 2023)
EndedAt: 2023-03-29 20:56:35 -0400 (Wed, 29 Mar 2023)
EllapsedTime: 627.7 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_1.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/INSPEcT.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.28.0’
* 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                  66.558  0.316  67.018
quantifyExpressionsFromBAMs     30.726 10.174  41.344
INSPEcT_diffsteady-class        24.079  0.267  24.401
compareSteady                   21.778  0.088  21.915
plotMA                          21.709  0.128  21.974
rocCurve                        20.935  0.128  21.095
makeSimModel                    20.764  0.112  20.917
rocThresholds                   20.502  0.115  20.657
quantifyExpressionsFromTrCounts 15.222  0.172  15.436
modelRates                      13.400  0.045  13.464
newINSPEcT                      13.168  0.049  13.251
processingDelay                 12.395  0.045  12.463
makeOscillatorySimModel          5.435  0.054   5.508
compareSteadyNoNascent           5.361  0.053   5.422
* 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-3.16-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/4.2/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-method0.1500.0070.157
Extract1.0110.0081.023
INSPEcT_diffsteady-class24.079 0.26724.401
calculateRatePvals0.1790.0020.183
chisqmodel0.1670.0020.170
chisqtest0.1630.0060.171
combine0.3340.0070.344
compareSteady21.778 0.08821.915
compareSteadyNoNascent5.3610.0535.422
convergence0.1900.0080.197
geneClass0.2320.0100.242
inHeatmap0.2200.0090.229
inspectFromPCR2.7550.0202.779
labeledSF0.1890.0090.198
logLik0.1770.0100.189
makeModelRates0.1970.0040.201
makeOscillatorySimModel5.4350.0545.508
makeSimDataset66.558 0.31667.018
makeSimModel20.764 0.11220.917
modelRates13.400 0.04513.464
modelRatesNF1.2160.0331.251
modelSelection0.1760.0080.188
modelingParams0.1500.0050.156
nGenes0.1860.0060.194
nTpts0.1820.0060.189
newINSPEcT13.168 0.04913.251
plotGene0.1980.0030.203
plotMA21.709 0.12821.974
processingDelay12.395 0.04512.463
quantifyExpressionsFromBAMs30.72610.17441.344
quantifyExpressionsFromTrCounts15.222 0.17215.436
ratePvals0.1860.0040.191
ratesFirstGuess0.1750.0050.181
ratesFirstGuessVar0.1880.0040.194
removeModel0.2560.0040.260
rocCurve20.935 0.12821.095
rocThresholds20.502 0.11520.657
split0.2370.0020.239
tpts0.1580.0020.162
viewConfidenceIntervals0.1480.0050.153
viewModelRates0.1610.0040.165