Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1040/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
INSPEcT 1.34.0 (landing page) Stefano de Pretis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.34.0 |
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_1.34.0.tar.gz |
StartedAt: 2024-06-24 06:13:36 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 06:50:19 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 2203.2 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/INSPEcT.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘INSPEcT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘INSPEcT’ version ‘1.34.0’ * 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 ... NOTE 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 ... OK * 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 239.496 1.664 292.281 modelRates 106.061 0.952 123.942 makeSimModel 82.793 0.615 100.044 rocCurve 81.685 0.743 97.983 rocThresholds 80.412 0.535 97.869 quantifyExpressionsFromBAMs 72.948 6.481 94.024 INSPEcT_diffsteady-class 74.594 0.861 93.066 plotMA 68.184 0.458 76.167 compareSteady 67.710 0.552 82.376 newINSPEcT 42.812 0.288 51.135 quantifyExpressionsFromTrCounts 36.488 0.331 42.642 processingDelay 35.367 0.416 38.761 makeOscillatorySimModel 19.991 0.229 23.635 inspectFromPCR 18.984 0.178 23.340 compareSteadyNoNascent 14.447 0.132 17.452 modelRatesNF 12.132 0.267 16.034 * 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-3.19-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/4.4-x86_64/Resources/library’ * installing *source* package ‘INSPEcT’ ... ** 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 | 0.366 | 0.022 | 0.489 | |
Extract | 0.838 | 0.051 | 1.107 | |
INSPEcT_diffsteady-class | 74.594 | 0.861 | 93.066 | |
calculateRatePvals | 0.489 | 0.018 | 0.653 | |
chisqmodel | 0.370 | 0.020 | 0.502 | |
chisqtest | 0.370 | 0.019 | 0.481 | |
combine | 0.796 | 0.012 | 0.931 | |
compareSteady | 67.710 | 0.552 | 82.376 | |
compareSteadyNoNascent | 14.447 | 0.132 | 17.452 | |
convergence | 0.369 | 0.020 | 0.473 | |
geneClass | 0.481 | 0.007 | 0.579 | |
inHeatmap | 0.451 | 0.020 | 0.564 | |
inspectFromPCR | 18.984 | 0.178 | 23.340 | |
labeledSF | 0.362 | 0.019 | 0.457 | |
logLik | 0.363 | 0.021 | 0.496 | |
makeModelRates | 0.488 | 0.013 | 0.654 | |
makeOscillatorySimModel | 19.991 | 0.229 | 23.635 | |
makeSimDataset | 239.496 | 1.664 | 292.281 | |
makeSimModel | 82.793 | 0.615 | 100.044 | |
modelRates | 106.061 | 0.952 | 123.942 | |
modelRatesNF | 12.132 | 0.267 | 16.034 | |
modelSelection | 0.366 | 0.017 | 0.472 | |
modelingParams | 0.365 | 0.017 | 0.476 | |
nGenes | 0.364 | 0.018 | 0.474 | |
nTpts | 0.366 | 0.019 | 0.481 | |
newINSPEcT | 42.812 | 0.288 | 51.135 | |
plotGene | 0.449 | 0.009 | 0.528 | |
plotMA | 68.184 | 0.458 | 76.167 | |
processingDelay | 35.367 | 0.416 | 38.761 | |
quantifyExpressionsFromBAMs | 72.948 | 6.481 | 94.024 | |
quantifyExpressionsFromTrCounts | 36.488 | 0.331 | 42.642 | |
ratePvals | 0.364 | 0.007 | 0.429 | |
ratesFirstGuess | 0.364 | 0.012 | 0.444 | |
ratesFirstGuessVar | 0.363 | 0.013 | 0.445 | |
removeModel | 0.618 | 0.009 | 0.743 | |
rocCurve | 81.685 | 0.743 | 97.983 | |
rocThresholds | 80.412 | 0.535 | 97.869 | |
split | 0.588 | 0.007 | 0.746 | |
tpts | 0.359 | 0.006 | 0.477 | |
viewConfidenceIntervals | 0.362 | 0.016 | 0.493 | |
viewModelRates | 0.363 | 0.008 | 0.465 | |