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

This page was generated on 2025-09-20 12:07 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1052/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.39.1  (landing page)
Stefano de Pretis
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: INSPEcT
Version: 1.39.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings INSPEcT_1.39.1.tar.gz
StartedAt: 2025-09-19 09:33:52 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 09:50:15 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 982.5 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings INSPEcT_1.39.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.39.1’
* 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                  115.796  0.371 119.152
quantifyExpressionsFromBAMs      43.110  0.187  51.574
INSPEcT_diffsteady-class         39.699  0.723  40.584
makeSimModel                     40.324  0.059  43.968
rocCurve                         38.664  0.091  40.405
rocThresholds                    38.543  0.163  39.319
plotMA                           35.533  0.052  36.408
compareSteady                    34.380  0.147  34.808
modelRates                       23.061  0.044  24.365
quantifyExpressionsFromTrCounts  20.944  0.127  21.137
newINSPEcT                       20.761  0.064  21.386
processingDelay                  19.617  0.179  20.137
makeOscillatorySimModel           9.337  0.044   9.606
compareSteadyNoNascent            7.660  0.080   7.802
inspectFromPCR                    5.099  0.012   5.189
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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-method0.1910.0040.196
Extract0.4360.0070.525
INSPEcT_diffsteady-class39.699 0.72340.584
calculateRatePvals0.2500.0200.271
chisqmodel0.1940.0000.194
chisqtest0.1920.0000.192
combine0.4450.0000.447
compareSteady34.380 0.14734.808
compareSteadyNoNascent7.6600.0807.802
convergence0.1930.0000.194
geneClass0.2510.0040.256
inHeatmap0.2400.0000.264
inspectFromPCR5.0990.0125.189
labeledSF0.1890.0080.374
logLik0.1950.0000.390
makeModelRates0.2530.0000.454
makeOscillatorySimModel9.3370.0449.606
makeSimDataset115.796 0.371119.152
makeSimModel40.324 0.05943.968
modelRates23.061 0.04424.365
modelRatesNF1.8260.0071.844
modelSelection0.1870.0000.187
modelingParams0.1860.0000.186
nGenes0.1820.0040.187
nTpts0.1870.0000.186
newINSPEcT20.761 0.06421.386
plotGene0.2430.0000.244
plotMA35.533 0.05236.408
processingDelay19.617 0.17920.137
quantifyExpressionsFromBAMs43.110 0.18751.574
quantifyExpressionsFromTrCounts20.944 0.12721.137
ratePvals0.1860.0000.186
ratesFirstGuess0.1850.0000.187
ratesFirstGuessVar0.1820.0040.187
removeModel0.3280.0000.343
rocCurve38.664 0.09140.405
rocThresholds38.543 0.16339.319
split0.3230.0000.326
tpts0.1790.0080.189
viewConfidenceIntervals0.1850.0030.190
viewModelRates0.1870.0000.190