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This page was generated on 2024-05-04 11:39:23 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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

Package 1040/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.34.0  (landing page)
Stefano de Pretis
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_19
git_last_commit: 455938d
git_last_commit_date: 2024-04-30 10:44:32 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for INSPEcT on lconway


To the developers/maintainers of the INSPEcT package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: INSPEcT
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.34.0.tar.gz
StartedAt: 2024-05-03 22:39:18 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:54:08 -0400 (Fri, 03 May 2024)
EllapsedTime: 889.6 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/INSPEcT.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.34.0’
* 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 code 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                  93.386  0.978  95.224
quantifyExpressionsFromBAMs     40.074  8.226  49.195
modelRates                      47.071  0.420  48.096
INSPEcT_diffsteady-class        33.231  0.481  33.960
rocCurve                        31.410  0.391  32.151
makeSimModel                    29.239  0.320  29.805
plotMA                          29.231  0.261  29.710
rocThresholds                   29.004  0.343  29.646
compareSteady                   28.284  0.316  28.870
quantifyExpressionsFromTrCounts 19.052  0.256  19.478
newINSPEcT                      17.646  0.212  18.079
processingDelay                 16.252  0.161  16.527
inspectFromPCR                   7.806  0.089   7.970
makeOscillatorySimModel          7.018  0.101   7.187
compareSteadyNoNascent           6.687  0.089   6.835
modelRatesNF                     5.441  0.115   5.617
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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-method0.2350.0140.252
Extract0.4730.0230.502
INSPEcT_diffsteady-class33.231 0.48133.960
calculateRatePvals0.2600.0100.274
chisqmodel0.2010.0110.214
chisqtest0.2130.0120.228
combine0.4290.0090.443
compareSteady28.284 0.31628.870
compareSteadyNoNascent6.6870.0896.835
convergence0.2010.0100.214
geneClass0.2640.0120.279
inHeatmap0.2500.0130.265
inspectFromPCR7.8060.0897.970
labeledSF0.2100.0090.222
logLik0.1970.0070.206
makeModelRates0.2520.0070.262
makeOscillatorySimModel7.0180.1017.187
makeSimDataset93.386 0.97895.224
makeSimModel29.239 0.32029.805
modelRates47.071 0.42048.096
modelRatesNF5.4410.1155.617
modelSelection0.2200.0090.231
modelingParams0.2020.0070.212
nGenes0.2230.0090.233
nTpts0.2010.0070.210
newINSPEcT17.646 0.21218.079
plotGene0.2400.0080.250
plotMA29.231 0.26129.710
processingDelay16.252 0.16116.527
quantifyExpressionsFromBAMs40.074 8.22649.195
quantifyExpressionsFromTrCounts19.052 0.25619.478
ratePvals0.1950.0040.200
ratesFirstGuess0.2100.0090.220
ratesFirstGuessVar0.2250.0080.235
removeModel0.3280.0060.337
rocCurve31.410 0.39132.151
rocThresholds29.004 0.34329.646
split0.3230.0050.331
tpts0.2120.0040.219
viewConfidenceIntervals0.1980.0090.209
viewModelRates0.2210.0060.230