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This page was generated on 2023-02-07 11:05:17 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 965/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.29.0  (landing page)
Stefano de Pretis
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: master
git_last_commit: 5409025
git_last_commit_date: 2022-11-01 11:11:51 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 1.29.0
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/library --timings INSPEcT_1.29.0.tar.gz
StartedAt: 2023-02-06 21:23:34 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 21:41:45 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 1090.9 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/library --timings INSPEcT_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-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 22.04.1 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  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                  74.803  0.576  75.452
modelRates                      36.061  0.175  36.237
INSPEcT_diffsteady-class        28.745  0.670  29.418
quantifyExpressionsFromBAMs     28.991  0.224  29.222
rocCurve                        24.321  0.055  24.378
makeSimModel                    24.224  0.040  24.264
rocThresholds                   23.991  0.060  24.052
compareSteady                   23.516  0.167  23.686
plotMA                          23.339  0.088  23.426
quantifyExpressionsFromTrCounts 15.526  0.093  15.618
processingDelay                 14.515  0.147  14.663
newINSPEcT                      14.218  0.047  14.266
inspectFromPCR                   6.123  0.013   6.136
makeOscillatorySimModel          5.776  0.048   5.827
compareSteadyNoNascent           5.362  0.008   5.371
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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-method0.1810.0080.190
Extract0.3500.0120.362
INSPEcT_diffsteady-class28.745 0.67029.418
calculateRatePvals0.2120.0090.220
chisqmodel0.1820.0000.182
chisqtest0.1770.0040.182
combine0.3380.0110.350
compareSteady23.516 0.16723.686
compareSteadyNoNascent5.3620.0085.371
convergence0.1780.0080.186
geneClass0.2130.0040.216
inHeatmap0.2160.0000.216
inspectFromPCR6.1230.0136.136
labeledSF0.1810.0040.186
logLik0.1820.0000.182
makeModelRates0.2150.0040.219
makeOscillatorySimModel5.7760.0485.827
makeSimDataset74.803 0.57675.452
makeSimModel24.224 0.04024.264
modelRates36.061 0.17536.237
modelRatesNF3.9760.0284.004
modelSelection0.180.000.18
modelingParams0.1760.0040.179
nGenes0.1790.0040.183
nTpts0.1750.0080.184
newINSPEcT14.218 0.04714.266
plotGene0.2270.0000.227
plotMA23.339 0.08823.426
processingDelay14.515 0.14714.663
quantifyExpressionsFromBAMs28.991 0.22429.222
quantifyExpressionsFromTrCounts15.526 0.09315.618
ratePvals0.1780.0000.178
ratesFirstGuess0.1770.0020.179
ratesFirstGuessVar0.1780.0020.179
removeModel0.2660.0040.270
rocCurve24.321 0.05524.378
rocThresholds23.991 0.06024.052
split0.2610.0000.261
tpts0.1770.0000.176
viewConfidenceIntervals0.180.000.18
viewModelRates0.1750.0040.179