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This page was generated on 2025-09-26 12:03 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1053/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.39.1  (landing page)
Stefano de Pretis
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 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 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-09-26 00:46:46 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 01:06:02 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 1155.4 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 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                  81.214  0.486  81.739
modelRates                      40.731  0.056  40.797
quantifyExpressionsFromBAMs     30.898  0.190  31.404
INSPEcT_diffsteady-class        29.857  0.599  30.469
makeSimModel                    26.633  0.161  26.795
rocCurve                        25.604  0.158  25.763
compareSteady                   25.273  0.128  25.413
plotMA                          25.013  0.024  25.042
rocThresholds                   24.617  0.105  24.722
newINSPEcT                      16.121  0.216  16.338
quantifyExpressionsFromTrCounts 16.181  0.108  16.290
processingDelay                 13.252  0.021  13.273
inspectFromPCR                   7.351  0.015   7.366
makeOscillatorySimModel          6.525  0.020   6.546
compareSteadyNoNascent           5.707  0.016   5.723
* 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-method0.1970.0070.204
Extract0.4200.0040.424
INSPEcT_diffsteady-class29.857 0.59930.469
calculateRatePvals0.2500.0130.263
chisqmodel0.2080.0050.213
chisqtest0.2140.0010.214
combine0.3840.0060.390
compareSteady25.273 0.12825.413
compareSteadyNoNascent5.7070.0165.723
convergence0.2070.0060.213
geneClass0.2480.0030.251
inHeatmap0.2650.0080.272
inspectFromPCR7.3510.0157.366
labeledSF0.2220.0000.222
logLik0.2570.0000.257
makeModelRates0.3190.0040.323
makeOscillatorySimModel6.5250.0206.546
makeSimDataset81.214 0.48681.739
makeSimModel26.633 0.16126.795
modelRates40.731 0.05640.797
modelRatesNF4.4600.0184.478
modelSelection0.2030.0040.207
modelingParams0.2030.0020.206
nGenes0.2070.0000.207
nTpts0.20.00.2
newINSPEcT16.121 0.21616.338
plotGene0.2470.0020.248
plotMA25.013 0.02425.042
processingDelay13.252 0.02113.273
quantifyExpressionsFromBAMs30.898 0.19031.404
quantifyExpressionsFromTrCounts16.181 0.10816.290
ratePvals0.1870.0000.187
ratesFirstGuess0.1850.0010.186
ratesFirstGuessVar0.1860.0000.186
removeModel0.2890.0000.290
rocCurve25.604 0.15825.763
rocThresholds24.617 0.10524.722
split0.2720.0020.274
tpts0.1840.0030.186
viewConfidenceIntervals0.1850.0030.188
viewModelRates0.1860.0010.187