Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1052/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
INSPEcT 1.38.0 (landing page) Stefano de Pretis
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: INSPEcT |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.38.0.tar.gz |
StartedAt: 2025-08-01 05:01:13 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 05:32:26 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 1872.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: INSPEcT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/INSPEcT.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘INSPEcT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘INSPEcT’ version ‘1.38.0’ * 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 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 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 226.095 1.252 240.697 modelRates 100.206 0.495 106.218 makeSimModel 78.480 0.409 82.885 rocThresholds 77.500 0.312 82.969 rocCurve 76.793 0.376 81.061 quantifyExpressionsFromBAMs 70.289 6.184 83.782 INSPEcT_diffsteady-class 70.430 0.551 79.176 plotMA 64.380 0.273 72.268 compareSteady 63.729 0.261 67.822 newINSPEcT 40.538 0.229 42.310 processingDelay 34.983 0.255 40.242 quantifyExpressionsFromTrCounts 34.517 0.210 37.583 makeOscillatorySimModel 18.941 0.146 19.568 inspectFromPCR 17.798 0.062 18.109 compareSteadyNoNascent 13.736 0.080 14.169 modelRatesNF 11.652 0.240 12.384 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/INSPEcT.Rcheck/00check.log’ for details.
INSPEcT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL INSPEcT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)
INSPEcT.Rcheck/INSPEcT-Ex.timings
name | user | system | elapsed | |
AIC-INSPEcT-method | 0.365 | 0.019 | 0.415 | |
Extract | 0.786 | 0.010 | 0.847 | |
INSPEcT_diffsteady-class | 70.430 | 0.551 | 79.176 | |
calculateRatePvals | 0.475 | 0.009 | 0.538 | |
chisqmodel | 0.357 | 0.007 | 0.396 | |
chisqtest | 0.354 | 0.008 | 0.394 | |
combine | 0.783 | 0.010 | 0.856 | |
compareSteady | 63.729 | 0.261 | 67.822 | |
compareSteadyNoNascent | 13.736 | 0.080 | 14.169 | |
convergence | 0.359 | 0.007 | 0.369 | |
geneClass | 0.477 | 0.008 | 0.486 | |
inHeatmap | 0.439 | 0.008 | 0.449 | |
inspectFromPCR | 17.798 | 0.062 | 18.109 | |
labeledSF | 0.347 | 0.003 | 0.350 | |
logLik | 0.364 | 0.007 | 0.372 | |
makeModelRates | 0.477 | 0.008 | 0.486 | |
makeOscillatorySimModel | 18.941 | 0.146 | 19.568 | |
makeSimDataset | 226.095 | 1.252 | 240.697 | |
makeSimModel | 78.480 | 0.409 | 82.885 | |
modelRates | 100.206 | 0.495 | 106.218 | |
modelRatesNF | 11.652 | 0.240 | 12.384 | |
modelSelection | 0.356 | 0.004 | 0.373 | |
modelingParams | 0.355 | 0.008 | 0.365 | |
nGenes | 0.356 | 0.003 | 0.363 | |
nTpts | 0.357 | 0.007 | 0.375 | |
newINSPEcT | 40.538 | 0.229 | 42.310 | |
plotGene | 0.436 | 0.006 | 0.467 | |
plotMA | 64.380 | 0.273 | 72.268 | |
processingDelay | 34.983 | 0.255 | 40.242 | |
quantifyExpressionsFromBAMs | 70.289 | 6.184 | 83.782 | |
quantifyExpressionsFromTrCounts | 34.517 | 0.210 | 37.583 | |
ratePvals | 0.359 | 0.004 | 0.403 | |
ratesFirstGuess | 0.356 | 0.011 | 0.400 | |
ratesFirstGuessVar | 0.358 | 0.009 | 0.396 | |
removeModel | 0.596 | 0.005 | 0.653 | |
rocCurve | 76.793 | 0.376 | 81.061 | |
rocThresholds | 77.500 | 0.312 | 82.969 | |
split | 0.562 | 0.003 | 0.567 | |
tpts | 0.353 | 0.004 | 0.363 | |
viewConfidenceIntervals | 0.358 | 0.014 | 0.374 | |
viewModelRates | 0.352 | 0.007 | 0.367 | |