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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 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: 2025-10-13 13:40 -0400 (Mon, 13 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 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 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: 2025-10-16 00:16:23 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 00:35:16 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 1132.7 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                  74.112  0.369  74.486
modelRates                      37.712  0.095  37.808
quantifyExpressionsFromBAMs     29.819  2.925  32.847
INSPEcT_diffsteady-class        28.041  0.624  28.667
rocThresholds                   25.611  0.190  25.802
makeSimModel                    24.955  0.131  25.086
rocCurve                        24.827  0.024  24.852
compareSteady                   23.094  0.197  23.292
plotMA                          22.942  0.018  22.959
quantifyExpressionsFromTrCounts 16.523  0.081  16.606
newINSPEcT                      13.671  0.106  13.777
processingDelay                 12.709  0.039  12.748
inspectFromPCR                   6.630  0.069   6.700
makeOscillatorySimModel          5.825  0.030   5.859
compareSteadyNoNascent           5.328  0.048   5.376
* 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

##############################################################################
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###
### 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-method0.1860.0090.197
Extract0.3790.0050.385
INSPEcT_diffsteady-class28.041 0.62428.667
calculateRatePvals0.2230.0010.224
chisqmodel0.1870.0010.188
chisqtest0.1860.0010.186
combine0.3450.0050.350
compareSteady23.094 0.19723.292
compareSteadyNoNascent5.3280.0485.376
convergence0.1870.0060.193
geneClass0.2230.0040.227
inHeatmap0.2220.0110.233
inspectFromPCR6.6300.0696.700
labeledSF0.1890.0050.194
logLik0.1850.0050.190
makeModelRates0.2210.0080.229
makeOscillatorySimModel5.8250.0305.859
makeSimDataset74.112 0.36974.486
makeSimModel24.955 0.13125.086
modelRates37.712 0.09537.808
modelRatesNF4.0190.0514.070
modelSelection0.1870.0040.190
modelingParams0.1870.0040.190
nGenes0.1860.0040.189
nTpts0.1850.0030.188
newINSPEcT13.671 0.10613.777
plotGene0.2250.0000.225
plotMA22.942 0.01822.959
processingDelay12.709 0.03912.748
quantifyExpressionsFromBAMs29.819 2.92532.847
quantifyExpressionsFromTrCounts16.523 0.08116.606
ratePvals0.1870.0000.187
ratesFirstGuess0.1860.0030.189
ratesFirstGuessVar0.1860.0030.190
removeModel0.2790.0020.281
rocCurve24.827 0.02424.852
rocThresholds25.611 0.19025.802
split0.2680.0010.268
tpts0.1850.0000.185
viewConfidenceIntervals0.1850.0040.188
viewModelRates0.1860.0010.186