Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-06 13:52 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1042/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.39.1  (landing page)
Stefano de Pretis
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 2025)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: devel
git_last_commit: 9163233
git_last_commit_date: 2025-07-22 21:29:21 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for INSPEcT on nebbiolo2

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: 1.39.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings INSPEcT_1.39.1.tar.gz
StartedAt: 2025-08-05 23:27:21 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-05 23:46:02 -0400 (Tue, 05 Aug 2025)
EllapsedTime: 1121.3 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings INSPEcT_1.39.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.39.1’
* 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 loading without being on the library search path ... 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                  74.365  0.477  74.843
modelRates                      38.548  0.215  38.764
quantifyExpressionsFromBAMs     32.420  0.188  32.950
INSPEcT_diffsteady-class        27.880  0.513  28.394
rocCurve                        25.220  0.084  25.304
rocThresholds                   24.647  0.090  24.738
makeSimModel                    24.075  0.040  24.115
plotMA                          23.624  0.057  23.681
compareSteady                   22.815  0.051  22.866
quantifyExpressionsFromTrCounts 16.455  0.001  16.457
newINSPEcT                      13.738  0.024  13.761
processingDelay                 13.616  0.065  13.681
inspectFromPCR                   6.610  0.048   6.659
makeOscillatorySimModel          5.803  0.049   5.853
compareSteadyNoNascent           5.325  0.049   5.375
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘INSPEcT’ ...
** this is package ‘INSPEcT’ version ‘1.39.1’
** 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-method0.1900.0070.198
Extract0.3610.0050.366
INSPEcT_diffsteady-class27.880 0.51328.394
calculateRatePvals0.2260.0050.231
chisqmodel0.1880.0010.189
chisqtest0.1850.0050.189
combine0.3500.0050.355
compareSteady22.815 0.05122.866
compareSteadyNoNascent5.3250.0495.375
convergence0.1870.0060.193
geneClass0.2230.0060.229
inHeatmap0.2200.0020.223
inspectFromPCR6.6100.0486.659
labeledSF0.1880.0060.194
logLik0.1900.0010.192
makeModelRates0.2270.0010.228
makeOscillatorySimModel5.8030.0495.853
makeSimDataset74.365 0.47774.843
makeSimModel24.075 0.04024.115
modelRates38.548 0.21538.764
modelRatesNF4.0790.0144.094
modelSelection0.1890.0000.189
modelingParams0.1870.0000.187
nGenes0.1870.0000.187
nTpts0.1880.0010.188
newINSPEcT13.738 0.02413.761
plotGene0.2260.0000.226
plotMA23.624 0.05723.681
processingDelay13.616 0.06513.681
quantifyExpressionsFromBAMs32.420 0.18832.950
quantifyExpressionsFromTrCounts16.455 0.00116.457
ratePvals0.1870.0000.187
ratesFirstGuess0.1860.0000.186
ratesFirstGuessVar0.1860.0010.186
removeModel0.280.000.28
rocCurve25.220 0.08425.304
rocThresholds24.647 0.09024.738
split0.2740.0020.277
tpts0.1840.0020.186
viewConfidenceIntervals0.1860.0010.187
viewModelRates0.1850.0010.187