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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-09 13:40 -0400 (Thu, 09 Oct 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 24.04.3 LTS) / x86_64  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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings INSPEcT_1.38.0.tar.gz
StartedAt: 2025-10-13 00:18:52 -0400 (Mon, 13 Oct 2025)
EndedAt: 2025-10-13 00:37:43 -0400 (Mon, 13 Oct 2025)
EllapsedTime: 1130.6 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings INSPEcT_1.38.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.3 LTS
* using session charset: UTF-8
* 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  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.9Mb
* 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                  74.000  0.340  74.342
modelRates                      37.879  0.090  37.969
quantifyExpressionsFromBAMs     29.512  1.326  30.930
INSPEcT_diffsteady-class        27.726  0.598  28.326
rocThresholds                   25.885  0.308  26.195
rocCurve                        25.092  0.368  25.461
makeSimModel                    25.103  0.134  25.239
compareSteady                   22.919  0.203  23.123
plotMA                          22.966  0.009  22.976
quantifyExpressionsFromTrCounts 16.639  0.459  17.101
newINSPEcT                      13.928  0.125  14.053
processingDelay                 12.709  0.032  12.741
inspectFromPCR                   6.585  0.084   6.670
makeOscillatorySimModel          5.761  0.023   5.786
compareSteadyNoNascent           5.252  0.049   5.301
* 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-3.21-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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-method0.2290.0080.238
Extract0.3750.0090.384
INSPEcT_diffsteady-class27.726 0.59828.326
calculateRatePvals0.2200.0030.223
chisqmodel0.1860.0020.188
chisqtest0.1840.0020.187
combine0.3530.0050.359
compareSteady22.919 0.20323.123
compareSteadyNoNascent5.2520.0495.301
convergence0.1890.0050.194
geneClass0.2250.0020.228
inHeatmap0.2210.0030.224
inspectFromPCR6.5850.0846.670
labeledSF0.1870.0070.194
logLik0.1870.0030.191
makeModelRates0.2220.0060.228
makeOscillatorySimModel5.7610.0235.786
makeSimDataset74.000 0.34074.342
makeSimModel25.103 0.13425.239
modelRates37.879 0.09037.969
modelRatesNF4.0660.0244.090
modelSelection0.1910.0010.192
modelingParams0.1840.0040.188
nGenes0.1820.0060.188
nTpts0.190.000.19
newINSPEcT13.928 0.12514.053
plotGene0.2240.0030.227
plotMA22.966 0.00922.976
processingDelay12.709 0.03212.741
quantifyExpressionsFromBAMs29.512 1.32630.930
quantifyExpressionsFromTrCounts16.639 0.45917.101
ratePvals0.1860.0100.196
ratesFirstGuess0.1880.0050.192
ratesFirstGuessVar0.1870.0040.192
removeModel0.2850.0060.292
rocCurve25.092 0.36825.461
rocThresholds25.885 0.30826.195
split0.2740.0040.277
tpts0.1850.0020.187
viewConfidenceIntervals0.1860.0040.190
viewModelRates0.1870.0020.189