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This page was generated on 2023-03-27 05:50:36 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
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CHECK results for INSPEcT on kunpeng1


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 986/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.29.0  (landing page)
Stefano de Pretis
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: devel
git_last_commit: 5409025
git_last_commit_date: 2022-11-01 15:11:51 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: INSPEcT
Version: 1.29.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings INSPEcT_1.29.0.tar.gz
StartedAt: 2023-03-25 05:04:14 -0000 (Sat, 25 Mar 2023)
EndedAt: 2023-03-25 05:26:45 -0000 (Sat, 25 Mar 2023)
EllapsedTime: 1350.9 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings INSPEcT_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* 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                  117.413  0.352 117.769
quantifyExpressionsFromBAMs      53.060  0.804  54.406
INSPEcT_diffsteady-class         41.436  0.338  41.776
rocThresholds                    40.436  0.236  40.673
rocCurve                         39.833  0.240  40.074
makeSimModel                     39.492  0.052  39.546
plotMA                           35.946  0.128  36.075
compareSteady                    35.823  0.072  35.897
modelRates                       23.966  0.104  24.072
quantifyExpressionsFromTrCounts  22.431  0.352  22.784
newINSPEcT                       21.435  0.020  21.457
processingDelay                  19.719  0.052  19.773
makeOscillatorySimModel           9.263  0.008   9.274
compareSteadyNoNascent            7.933  0.056   7.989
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘INSPEcT.Rmd’ using ‘UTF-8’... OK
  ‘INSPEcT_GUI.rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.



Installation output

INSPEcT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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-method0.2220.0040.227
Extract0.4730.0040.477
INSPEcT_diffsteady-class41.436 0.33841.776
calculateRatePvals0.2800.0000.281
chisqmodel0.2250.0000.225
chisqtest0.2240.0000.224
combine0.4640.0000.463
compareSteady35.823 0.07235.897
compareSteadyNoNascent7.9330.0567.989
convergence0.2230.0000.224
geneClass0.2740.0080.282
inHeatmap0.2580.0080.266
inspectFromPCR4.8780.0084.887
labeledSF0.2110.0120.224
logLik0.2120.0120.224
makeModelRates0.2720.0080.281
makeOscillatorySimModel9.2630.0089.274
makeSimDataset117.413 0.352117.769
makeSimModel39.492 0.05239.546
modelRates23.966 0.10424.072
modelRatesNF1.8590.0281.887
modelSelection0.2220.0000.222
modelingParams0.2210.0000.221
nGenes0.2210.0000.221
nTpts0.2190.0000.219
newINSPEcT21.435 0.02021.457
plotGene0.2620.0080.270
plotMA35.946 0.12836.075
processingDelay19.719 0.05219.773
quantifyExpressionsFromBAMs53.060 0.80454.406
quantifyExpressionsFromTrCounts22.431 0.35222.784
ratePvals0.2230.0000.223
ratesFirstGuess0.2210.0000.221
ratesFirstGuessVar0.2210.0000.221
removeModel0.350.000.35
rocCurve39.833 0.24040.074
rocThresholds40.436 0.23640.673
split0.3550.0000.355
tpts0.2230.0000.223
viewConfidenceIntervals0.2260.0000.226
viewModelRates0.2220.0000.223