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This page was generated on 2023-01-02 09:00:34 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the INSPEcT package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 963/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.29.0  (landing page)
Stefano de Pretis
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
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)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: INSPEcT
Version: 1.29.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:INSPEcT.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings INSPEcT_1.29.0.tar.gz
StartedAt: 2022-12-29 00:41:20 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 00:47:21 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 361.0 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:INSPEcT.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings INSPEcT_1.29.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/INSPEcT.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'INSPEcT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'INSPEcT' version '1.29.0'
* 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 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
makeSimModel                    21.28   0.18   21.45
quantifyExpressionsFromTrCounts 14.07   0.14   14.20
newINSPEcT                      13.21   0.10   13.30
processingDelay                 11.39   0.22   11.61
compareSteadyNoNascent           6.36   0.13    6.48
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/INSPEcT.Rcheck/00check.log'
for details.



Installation output

INSPEcT.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL INSPEcT
###
##############################################################################
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* installing to library 'F:/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-method0.160.000.21
Extract0.310.000.31
INSPEcT_diffsteady-class000
calculateRatePvals0.190.010.20
chisqmodel0.140.000.14
chisqtest0.190.000.19
combine0.290.000.30
compareSteady000
compareSteadyNoNascent6.360.136.48
convergence0.160.000.16
geneClass0.170.000.17
inHeatmap0.170.000.17
inspectFromPCR0.000.010.02
labeledSF0.140.000.14
logLik0.130.020.14
makeModelRates0.190.000.19
makeOscillatorySimModel4.950.014.98
makeSimDataset000
makeSimModel21.28 0.1821.45
modelRates000
modelRatesNF000
modelSelection0.140.010.16
modelingParams0.160.000.16
nGenes0.140.000.14
nTpts0.120.010.14
newINSPEcT13.21 0.1013.30
plotGene0.150.010.17
plotMA000
processingDelay11.39 0.2211.61
quantifyExpressionsFromBAMs000
quantifyExpressionsFromTrCounts14.07 0.1414.20
ratePvals0.140.000.14
ratesFirstGuess0.140.020.16
ratesFirstGuessVar0.170.000.17
removeModel0.220.000.22
rocCurve0.010.000.02
rocThresholds000
split0.220.000.22
tpts0.160.000.15
viewConfidenceIntervals0.140.010.16
viewModelRates0.140.000.14