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This page was generated on 2022-06-27 11:09:58 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 nebbiolo1


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: 2022-06-26 13:55:11 -0400 (Sun, 26 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

Summary

Package: INSPEcT
Version: 1.26.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings INSPEcT_1.26.0.tar.gz
StartedAt: 2022-06-26 20:20:30 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:31:54 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 684.6 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings INSPEcT_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/INSPEcT.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.9Mb
* 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                  70.530  0.448  70.981
modelRates                      33.627  0.124  33.751
quantifyExpressionsFromBAMs     30.962  0.300  31.267
INSPEcT_diffsteady-class        26.722  0.663  27.421
makeSimModel                    23.736  0.080  23.817
plotMA                          23.637  0.140  23.778
rocCurve                        23.235  0.052  23.287
rocThresholds                   23.006  0.044  23.051
compareSteady                   22.531  0.172  22.708
quantifyExpressionsFromTrCounts 15.038  0.076  15.114
newINSPEcT                      13.743  0.012  13.754
processingDelay                 12.986  0.076  13.061
inspectFromPCR                   6.199  0.048   6.252
makeOscillatorySimModel          5.712  0.056   5.770
compareSteadyNoNascent           5.324  0.032   5.355
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.



Installation output

INSPEcT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-method1.0400.0541.096
Extract0.3420.0040.346
INSPEcT_diffsteady-class26.722 0.66327.421
calculateRatePvals0.2070.0080.216
chisqmodel0.1790.0000.179
chisqtest0.1790.0000.179
combine0.3310.0040.334
compareSteady22.531 0.17222.708
compareSteadyNoNascent5.3240.0325.355
convergence0.1720.0100.181
geneClass0.2020.0100.212
inHeatmap0.2160.0000.215
inspectFromPCR6.1990.0486.252
labeledSF0.1710.0120.183
logLik0.1750.0040.180
makeModelRates0.2090.0040.213
makeOscillatorySimModel5.7120.0565.770
makeSimDataset70.530 0.44870.981
makeSimModel23.736 0.08023.817
modelRates33.627 0.12433.751
modelRatesNF3.9070.0203.926
modelSelection0.1660.0040.169
modelingParams0.1700.0040.173
nGenes0.1700.0040.175
nTpts0.1760.0000.177
newINSPEcT13.743 0.01213.754
plotGene0.2150.0000.214
plotMA23.637 0.14023.778
processingDelay12.986 0.07613.061
quantifyExpressionsFromBAMs30.962 0.30031.267
quantifyExpressionsFromTrCounts15.038 0.07615.114
ratePvals0.1750.0040.180
ratesFirstGuess0.1790.0000.180
ratesFirstGuessVar0.1720.0070.178
removeModel0.2700.0040.274
rocCurve23.235 0.05223.287
rocThresholds23.006 0.04423.051
split0.2600.0040.263
tpts0.1720.0000.172
viewConfidenceIntervals0.1760.0040.181
viewModelRates0.1750.0000.175