Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1052/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.38.0  (landing page)
Stefano de Pretis
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_21
git_last_commit: 7870789
git_last_commit_date: 2025-04-15 10:51:53 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for INSPEcT on merida1

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: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2025-08-01 05:01:13 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 05:32:26 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 1872.5 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/INSPEcT.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.38.0’
* 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 ... INFO
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  INSPEcT-class.Rd: featureNames
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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                  226.095  1.252 240.697
modelRates                      100.206  0.495 106.218
makeSimModel                     78.480  0.409  82.885
rocThresholds                    77.500  0.312  82.969
rocCurve                         76.793  0.376  81.061
quantifyExpressionsFromBAMs      70.289  6.184  83.782
INSPEcT_diffsteady-class         70.430  0.551  79.176
plotMA                           64.380  0.273  72.268
compareSteady                    63.729  0.261  67.822
newINSPEcT                       40.538  0.229  42.310
processingDelay                  34.983  0.255  40.242
quantifyExpressionsFromTrCounts  34.517  0.210  37.583
makeOscillatorySimModel          18.941  0.146  19.568
inspectFromPCR                   17.798  0.062  18.109
compareSteadyNoNascent           13.736  0.080  14.169
modelRatesNF                     11.652  0.240  12.384
* 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-3.21-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘INSPEcT’ ...
** this is package ‘INSPEcT’ version ‘1.38.0’
** 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-method0.3650.0190.415
Extract0.7860.0100.847
INSPEcT_diffsteady-class70.430 0.55179.176
calculateRatePvals0.4750.0090.538
chisqmodel0.3570.0070.396
chisqtest0.3540.0080.394
combine0.7830.0100.856
compareSteady63.729 0.26167.822
compareSteadyNoNascent13.736 0.08014.169
convergence0.3590.0070.369
geneClass0.4770.0080.486
inHeatmap0.4390.0080.449
inspectFromPCR17.798 0.06218.109
labeledSF0.3470.0030.350
logLik0.3640.0070.372
makeModelRates0.4770.0080.486
makeOscillatorySimModel18.941 0.14619.568
makeSimDataset226.095 1.252240.697
makeSimModel78.480 0.40982.885
modelRates100.206 0.495106.218
modelRatesNF11.652 0.24012.384
modelSelection0.3560.0040.373
modelingParams0.3550.0080.365
nGenes0.3560.0030.363
nTpts0.3570.0070.375
newINSPEcT40.538 0.22942.310
plotGene0.4360.0060.467
plotMA64.380 0.27372.268
processingDelay34.983 0.25540.242
quantifyExpressionsFromBAMs70.289 6.18483.782
quantifyExpressionsFromTrCounts34.517 0.21037.583
ratePvals0.3590.0040.403
ratesFirstGuess0.3560.0110.400
ratesFirstGuessVar0.3580.0090.396
removeModel0.5960.0050.653
rocCurve76.793 0.37681.061
rocThresholds77.500 0.31282.969
split0.5620.0030.567
tpts0.3530.0040.363
viewConfidenceIntervals0.3580.0140.374
viewModelRates0.3520.0070.367