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This page was generated on 2022-01-24 13:05:13 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 nebbiolo2


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? here 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 936/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.24.0  (landing page)
Stefano de Pretis
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_14
git_last_commit: ed551fb
git_last_commit_date: 2021-10-26 12:21:19 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: INSPEcT
Version: 1.24.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings INSPEcT_1.24.0.tar.gz
StartedAt: 2022-01-23 08:13:42 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 08:25:22 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 700.9 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings INSPEcT_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/INSPEcT.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.24.0’
* 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                  73.936  0.116  74.053
modelRates                      36.238  0.072  36.311
quantifyExpressionsFromBAMs     33.427  0.140  33.880
INSPEcT_diffsteady-class        32.777  0.291  33.081
compareSteady                   30.436  0.056  30.491
plotMA                          29.346  0.039  29.387
makeSimModel                    24.250  0.032  24.282
rocThresholds                   24.000  0.028  24.029
rocCurve                        23.819  0.032  23.852
quantifyExpressionsFromTrCounts 20.836  0.032  20.868
processingDelay                 18.664  0.024  18.689
newINSPEcT                      18.442  0.068  18.511
compareSteadyNoNascent           8.142  0.011   8.154
inspectFromPCR                   5.948  0.012   5.961
makeOscillatorySimModel          5.537  0.023   5.563
* 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-3.14-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.



Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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-method0.1870.0010.187
Extract0.4600.0080.467
INSPEcT_diffsteady-class32.777 0.29133.081
calculateRatePvals0.2140.0000.214
chisqmodel0.1740.0040.178
chisqtest0.180.000.18
combine0.3460.0040.350
compareSteady30.436 0.05630.491
compareSteadyNoNascent8.1420.0118.154
convergence0.1770.0000.178
geneClass0.2130.0000.214
inHeatmap0.2040.0080.213
inspectFromPCR5.9480.0125.961
labeledSF0.1710.0070.179
logLik0.1750.0010.175
makeModelRates0.2090.0000.210
makeOscillatorySimModel5.5370.0235.563
makeSimDataset73.936 0.11674.053
makeSimModel24.250 0.03224.282
modelRates36.238 0.07236.311
modelRatesNF4.2470.0324.280
modelSelection0.1720.0000.173
modelingParams0.1730.0000.173
nGenes0.1740.0000.174
nTpts0.1760.0000.176
newINSPEcT18.442 0.06818.511
plotGene0.2110.0000.211
plotMA29.346 0.03929.387
processingDelay18.664 0.02418.689
quantifyExpressionsFromBAMs33.427 0.14033.880
quantifyExpressionsFromTrCounts20.836 0.03220.868
ratePvals0.1740.0000.173
ratesFirstGuess0.1750.0000.174
ratesFirstGuessVar0.1750.0000.175
removeModel0.2630.0000.262
rocCurve23.819 0.03223.852
rocThresholds24.000 0.02824.029
split0.2540.0000.254
tpts0.1760.0000.176
viewConfidenceIntervals0.1770.0000.177
viewModelRates0.1760.0000.176