Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-18 11:47 -0400 (Mon, 18 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
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 24.04.3 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: INSPEcT |
Version: 1.38.0 |
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_1.38.0.tar.gz |
StartedAt: 2025-08-15 10:35:31 -0000 (Fri, 15 Aug 2025) |
EndedAt: 2025-08-15 10:52:38 -0000 (Fri, 15 Aug 2025) |
EllapsedTime: 1027.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: INSPEcT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/INSPEcT.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * 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 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 123.584 0.531 124.378 quantifyExpressionsFromBAMs 48.463 0.276 49.558 INSPEcT_diffsteady-class 43.070 0.788 43.948 rocThresholds 41.137 0.076 41.303 rocCurve 41.066 0.135 41.288 makeSimModel 40.854 0.067 41.009 plotMA 38.806 0.248 39.139 compareSteady 36.810 0.252 37.135 modelRates 24.722 0.108 24.878 quantifyExpressionsFromTrCounts 22.462 0.048 22.555 newINSPEcT 21.785 0.028 21.859 processingDelay 19.816 0.055 19.916 makeOscillatorySimModel 9.869 0.052 9.946 compareSteadyNoNascent 7.811 0.032 7.857 inspectFromPCR 5.171 0.032 5.217 * 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-3.21-bioc/meat/INSPEcT.Rcheck/00check.log’ for details.
INSPEcT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL INSPEcT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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)
INSPEcT.Rcheck/INSPEcT-Ex.timings
name | user | system | elapsed | |
AIC-INSPEcT-method | 0.185 | 0.012 | 0.200 | |
Extract | 0.486 | 0.004 | 0.491 | |
INSPEcT_diffsteady-class | 43.070 | 0.788 | 43.948 | |
calculateRatePvals | 0.252 | 0.010 | 0.263 | |
chisqmodel | 0.193 | 0.004 | 0.197 | |
chisqtest | 0.188 | 0.007 | 0.195 | |
combine | 0.454 | 0.016 | 0.470 | |
compareSteady | 36.810 | 0.252 | 37.135 | |
compareSteadyNoNascent | 7.811 | 0.032 | 7.857 | |
convergence | 0.193 | 0.004 | 0.197 | |
geneClass | 0.259 | 0.000 | 0.260 | |
inHeatmap | 0.240 | 0.008 | 0.248 | |
inspectFromPCR | 5.171 | 0.032 | 5.217 | |
labeledSF | 0.191 | 0.004 | 0.196 | |
logLik | 0.196 | 0.000 | 0.196 | |
makeModelRates | 0.256 | 0.004 | 0.260 | |
makeOscillatorySimModel | 9.869 | 0.052 | 9.946 | |
makeSimDataset | 123.584 | 0.531 | 124.378 | |
makeSimModel | 40.854 | 0.067 | 41.009 | |
modelRates | 24.722 | 0.108 | 24.878 | |
modelRatesNF | 1.834 | 0.012 | 1.849 | |
modelSelection | 0.191 | 0.004 | 0.196 | |
modelingParams | 0.228 | 0.000 | 0.228 | |
nGenes | 0.197 | 0.000 | 0.197 | |
nTpts | 0.195 | 0.000 | 0.195 | |
newINSPEcT | 21.785 | 0.028 | 21.859 | |
plotGene | 0.264 | 0.004 | 0.269 | |
plotMA | 38.806 | 0.248 | 39.139 | |
processingDelay | 19.816 | 0.055 | 19.916 | |
quantifyExpressionsFromBAMs | 48.463 | 0.276 | 49.558 | |
quantifyExpressionsFromTrCounts | 22.462 | 0.048 | 22.555 | |
ratePvals | 0.192 | 0.004 | 0.197 | |
ratesFirstGuess | 0.191 | 0.004 | 0.195 | |
ratesFirstGuessVar | 0.187 | 0.008 | 0.195 | |
removeModel | 0.343 | 0.004 | 0.346 | |
rocCurve | 41.066 | 0.135 | 41.288 | |
rocThresholds | 41.137 | 0.076 | 41.303 | |
split | 0.335 | 0.000 | 0.336 | |
tpts | 0.194 | 0.000 | 0.195 | |
viewConfidenceIntervals | 0.190 | 0.004 | 0.195 | |
viewModelRates | 0.189 | 0.004 | 0.193 | |