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This page was generated on 2025-09-30 12:07 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1054/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.39.1  (landing page)
Stefano de Pretis
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 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: 2025-09-30 09:23:36 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 09:39:45 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 969.3 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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                  116.686  0.459 117.451
quantifyExpressionsFromBAMs      43.487  0.279  44.674
INSPEcT_diffsteady-class         39.885  0.748  40.734
makeSimModel                     39.342  0.136  39.601
rocCurve                         38.776  0.096  38.978
rocThresholds                    38.671  0.195  38.970
plotMA                           35.067  0.095  35.252
compareSteady                    34.309  0.223  34.619
modelRates                       22.679  0.024  22.773
quantifyExpressionsFromTrCounts  21.135  0.155  21.357
newINSPEcT                       20.762  0.048  20.853
processingDelay                  19.141  0.136  19.323
makeOscillatorySimModel           9.289  0.067   9.387
compareSteadyNoNascent            7.707  0.036   7.764
* 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-method0.1870.0040.195
Extract0.4380.0040.443
INSPEcT_diffsteady-class39.885 0.74840.734
calculateRatePvals0.2470.0060.254
chisqmodel0.2050.0000.205
chisqtest0.1890.0000.189
combine0.4290.0040.433
compareSteady34.309 0.22334.619
compareSteadyNoNascent7.7070.0367.764
convergence0.1890.0000.189
geneClass0.2470.0040.252
inHeatmap0.2290.0080.237
inspectFromPCR4.9340.0164.966
labeledSF0.1890.0000.190
logLik0.1870.0040.191
makeModelRates0.2570.0000.258
makeOscillatorySimModel9.2890.0679.387
makeSimDataset116.686 0.459117.451
makeSimModel39.342 0.13639.601
modelRates22.679 0.02422.773
modelRatesNF1.8440.0081.856
modelSelection0.190.000.19
modelingParams0.1850.0040.189
nGenes0.1890.0000.191
nTpts0.1920.0000.192
newINSPEcT20.762 0.04820.853
plotGene0.2470.0000.247
plotMA35.067 0.09535.252
processingDelay19.141 0.13619.323
quantifyExpressionsFromBAMs43.487 0.27944.674
quantifyExpressionsFromTrCounts21.135 0.15521.357
ratePvals0.1860.0000.186
ratesFirstGuess0.1870.0000.187
ratesFirstGuessVar0.1870.0000.188
removeModel0.3490.0000.351
rocCurve38.776 0.09638.978
rocThresholds38.671 0.19538.970
split0.3260.0000.326
tpts0.1860.0030.190
viewConfidenceIntervals0.1830.0080.191
viewModelRates0.1900.0000.191