Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1514/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
peakPantheR 1.21.0 (landing page) Arnaud Wolfer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the peakPantheR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peakPantheR.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: peakPantheR |
Version: 1.21.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings peakPantheR_1.21.0.tar.gz |
StartedAt: 2024-12-22 20:42:20 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 20:50:40 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 500.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: peakPantheR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings peakPantheR_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/peakPantheR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘peakPantheR/DESCRIPTION’ ... OK * this is package ‘peakPantheR’ version ‘1.21.0’ * package encoding: UTF-8 * 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 ‘peakPantheR’ can be installed ... OK * checking installed package size ... OK * 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 whether startup messages can be suppressed ... 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed peakPantheR_ROIStatistics 8.558 0.065 8.670 peakPantheR_parallelAnnotation 6.651 0.032 6.692 outputAnnotationDiagnostic-peakPantheRAnnotation-method 6.571 0.026 6.656 outputAnnotationResult-peakPantheRAnnotation-method 6.319 0.019 6.357 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Error: Test failures In addition: Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 10 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 5: In .Internal(gc(verbose, reset, full)) : closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML) 6: In .Internal(gc(verbose, reset, full)) : closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML) Execution halted * 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: 1 ERROR See ‘/Users/biocbuild/bbs-3.21-bioc/meat/peakPantheR.Rcheck/00check.log’ for details.
peakPantheR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘peakPantheR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (peakPantheR)
peakPantheR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(peakPantheR) This is peakPantheR version 1.21.0 > > test_check("peakPantheR") 2024-12-22 20:45:37.078 R[18031:162937661] XType: Using static font registry. 2024-12-22 20:45:41.253 R[29855:162962094] XType: Using static font registry. 2024-12-22 20:45:43.937 R[30307:162962936] XType: Using static font registry. 2024-12-22 20:47:18.302 R[42101:162992405] XType: Using static font registry. [ FAIL 11 | WARN 0 | SKIP 0 | PASS 1467 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_findTargetFeatures.R:236:3'): ratio of fit residuals at apex or across maximum is superior to "maxApexResidualRatio", fit is rejected, verbose ── result_foundPeaks$result not equal to `expected_foundPeaks`. Component "peakTable": Component "found": 1 element mismatch Component "peakTable": Component "rtMin": 'is.NA' value mismatch: 1 in current 0 in target Component "peakTable": Component "rt": 'is.NA' value mismatch: 1 in current 0 in target Component "peakTable": Component "rtMax": 'is.NA' value mismatch: 1 in current 0 in target Component "peakTable": Component "mzMin": 'is.NA' value mismatch: 1 in current 0 in target Component "peakTable": Component "mz": 'is.NA' value mismatch: 1 in current 0 in target Component "peakTable": Component "mzMax": 'is.NA' value mismatch: 1 in current 0 in target Component "peakTable": Component "peakArea": 'is.NA' value mismatch: 1 in current 0 in target Component "peakTable": Component "peakAreaRaw": 'is.NA' value mismatch: 1 in current 0 in target ... ── Failure ('test_findTargetFeatures.R:239:3'): ratio of fit residuals at apex or across maximum is superior to "maxApexResidualRatio", fit is rejected, verbose ── length(result_foundPeaks$messages) not equal to 5. 1/1 mismatches [1] 4 - 5 == -1 ── Failure ('test_findTargetFeatures.R:240:3'): ratio of fit residuals at apex or across maximum is superior to "maxApexResidualRatio", fit is rejected, verbose ── result_foundPeaks$messages[1:4] not equal to `expected_messages`. 2/4 mismatches x[3]: "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/ x[3]: mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax fo x[3]: r ROI #4\n" y[3]: "Fit of ROI #3 is unsuccessful (apex residuals is 0.45 of max fit intensit y[3]: y, max intensity residuals is 0.46 of max fit intensity)\n" x[4]: "Found 4/4 features in 0.01 secs\n" y[4]: "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/ y[4]: mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax fo y[4]: r ROI #4\n" ── Failure ('test_fitCurve.R:55:3'): fit emgGaussian, input params ───────────── `result_fit` not equal to `expected_fit`. Component "amplitude": Mean relative difference: 0.0498193 Component "center": Mean relative difference: 8.406796e-05 Component "gamma": Mean relative difference: 0.03903418 ── Failure ('test_peakPantheR_ROIStatistics.R:77:3'): 3 files, save EICS, mean IS RT, save IS fit, with sampleColour, verbose, no verbose ── length(result_ROIstatsV$messages) not equal to 64. 1/1 mismatches [1] 63 - 64 == -1 ── Failure ('test_peakPantheR_ROIStatistics.R:78:3'): 3 files, save EICS, mean IS RT, save IS fit, with sampleColour, verbose, no verbose ── ...[] not equal to `expected_message`. 4/23 mismatches x[20]: "----------------\n" y[20]: "Annotation object cannot be reordered by sample acquisition date\n" x[21]: "Parallel annotation done in: 6.78 secs\n" y[21]: "----------------\n" x[22]: "Annotation parameters saved at /private/var/folders/r0/l4fjk6cj5xj0j3brt4 x[22]: bplpl40000gt/T/RtmpaOYCyq/IS_search/annotationParameters_summary.csv\n" y[22]: " 0 failure(s)\n" x[23]: " Compound 1/4 diagnostic plot saved at /private/var/folders/r0/l4fjk6cj5 x[23]: xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/IS_search/cpd_1.png\n" y[23]: "Saving diagnostic plots:\n" ── Failure ('test_peakPantheR_ROIStatistics.R:156:3'): 3 files, no save EICs, mean IS RT, no IS fit, without sampleColour, verbose, no verbose ── length(result_ROIstatsV$messages) not equal to 47. 1/1 mismatches [1] 46 - 47 == -1 ── Failure ('test_peakPantheR_ROIStatistics.R:157:3'): 3 files, no save EICs, mean IS RT, no IS fit, without sampleColour, verbose, no verbose ── result_ROIstatsV$messages[c(1:2, 4:12, 44, 46)] not equal to `expected_message`. 2/13 mismatches x[12]: "Parallel annotation done in: 6.67 secs\n" y[12]: "----------------\n" x[13]: "IS mean RT saved at /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000g x[13]: t/T/RtmpaOYCyq/IS_mean_RT.csv\n" y[13]: " 0 failure(s)\n" ── Failure ('test_peakPantheR_parallelAnnotation.R:138:3'): 3 files, 4 compounds, no uROI, no FIR, no getAcquTime, no verbose ── result_parallelAnnotation$result$annotation not equal to `expected_annotation`. Attributes: < Component "peakFit": Component 3: Component 3: Modes: list, logical > Attributes: < Component "peakFit": Component 3: Component 3: names for target but not for current > Attributes: < Component "peakFit": Component 3: Component 3: Attributes: < Modes: list, NULL > > Attributes: < Component "peakFit": Component 3: Component 3: Attributes: < names for target but not for current > > Attributes: < Component "peakFit": Component 3: Component 3: Attributes: < current is not list-like > > Attributes: < Component "peakFit": Component 3: Component 3: Length mismatch: comparison on first 1 components > Attributes: < Component "peakFit": Component 3: Component 3: Component 1: Modes: numeric, logical > Attributes: < Component "peakFit": Component 3: Component 3: Component 1: target is numeric, current is logical > Attributes: < Component "peakTables": Component 3: Component 1: 1 element mismatch > ... ── Failure ('test_peakPantheR_parallelAnnotation.R:171:3'): 3 files (1 missing), 4 compounds, no uROI, no FIR, no getAcquTime, no verbose ── result_parallelAnnotation$result$annotation not equal to `expected_annotation`. Attributes: < Component "peakFit": Component 2: Component 3: Modes: list, logical > Attributes: < Component "peakFit": Component 2: Component 3: names for target but not for current > Attributes: < Component "peakFit": Component 2: Component 3: Attributes: < Modes: list, NULL > > Attributes: < Component "peakFit": Component 2: Component 3: Attributes: < names for target but not for current > > Attributes: < Component "peakFit": Component 2: Component 3: Attributes: < current is not list-like > > Attributes: < Component "peakFit": Component 2: Component 3: Length mismatch: comparison on first 1 components > Attributes: < Component "peakFit": Component 2: Component 3: Component 1: Modes: numeric, logical > Attributes: < Component "peakFit": Component 2: Component 3: Component 1: target is numeric, current is logical > Attributes: < Component "peakTables": Component 2: Component 1: 1 element mismatch > ... ── Failure ('test_peakPantheR_parallelAnnotation.R:364:3'): 3 files, 4 compounds, uROI, no FIR, no fitGauss, no getAcquTime, no verbose ── result_parallelAnnotation$result$annotation not equal to `expected_annotation`. Attributes: < Component "peakFit": Component 3: Component 3: Modes: list, logical > Attributes: < Component "peakFit": Component 3: Component 3: names for target but not for current > Attributes: < Component "peakFit": Component 3: Component 3: Attributes: < Modes: list, NULL > > Attributes: < Component "peakFit": Component 3: Component 3: Attributes: < names for target but not for current > > Attributes: < Component "peakFit": Component 3: Component 3: Attributes: < current is not list-like > > Attributes: < Component "peakFit": Component 3: Component 3: Length mismatch: comparison on first 1 components > Attributes: < Component "peakFit": Component 3: Component 3: Component 1: Modes: numeric, logical > Attributes: < Component "peakFit": Component 3: Component 3: Component 1: target is numeric, current is logical > Attributes: < Component "peakTables": Component 3: Component 1: 1 element mismatch > ... [ FAIL 11 | WARN 0 | SKIP 0 | PASS 1467 ] Error: Test failures In addition: Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 10 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaOYCyq/notValidXML.mzML) 5: In .Internal(gc(verbose, reset, full)) : closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML) 6: In .Internal(gc(verbose, reset, full)) : closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML) Execution halted
peakPantheR.Rcheck/peakPantheR-Ex.timings
name | user | system | elapsed | |
EICs-peakPantheRAnnotation-method | 4.472 | 0.140 | 4.630 | |
FIR-peakPantheRAnnotation-method | 0.008 | 0.000 | 0.009 | |
ROI-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.007 | |
TIC-peakPantheRAnnotation-method | 0.006 | 0.000 | 0.006 | |
acquisitionTime-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.007 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.006 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.006 | 0.000 | 0.006 | |
annotationTable-peakPantheRAnnotation-method | 0.005 | 0.001 | 0.007 | |
annotation_diagnostic_multiplot_UI_helper | 0.049 | 0.002 | 0.052 | |
annotation_fit_summary_UI_helper | 0.002 | 0.000 | 0.002 | |
annotation_showMethod_UI_helper | 0.001 | 0.000 | 0.002 | |
annotation_showText_UI_helper | 0.001 | 0.001 | 0.000 | |
cpdID-peakPantheRAnnotation-method | 0.006 | 0.000 | 0.008 | |
cpdMetadata-peakPantheRAnnotation-method | 0.006 | 0.000 | 0.006 | |
cpdName-peakPantheRAnnotation-method | 0.005 | 0.001 | 0.005 | |
dataPoints-peakPantheRAnnotation-method | 0.005 | 0.000 | 0.006 | |
filename-peakPantheRAnnotation-method | 0.005 | 0.001 | 0.005 | |
filepath-peakPantheRAnnotation-method | 0.005 | 0.000 | 0.005 | |
initialise_annotation_from_files_UI_helper | 0.004 | 0.000 | 0.004 | |
isAnnotated-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.006 | |
load_annotation_from_file_UI_helper | 0.002 | 0.000 | 0.002 | |
nbCompounds-peakPantheRAnnotation-method | 0.005 | 0.001 | 0.006 | |
nbSamples-peakPantheRAnnotation-method | 0.005 | 0.000 | 0.006 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 6.571 | 0.026 | 6.656 | |
outputAnnotationFeatureMetadata_UI_helper | 0.002 | 0.000 | 0.002 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.007 | 0.000 | 0.008 | |
outputAnnotationResult-peakPantheRAnnotation-method | 6.319 | 0.019 | 6.357 | |
outputAnnotationSpectraMetadata_UI_helper | 0.002 | 0.000 | 0.002 | |
peakFit-peakPantheRAnnotation-method | 0.007 | 0.001 | 0.008 | |
peakPantheRAnnotation | 0.009 | 0.000 | 0.010 | |
peakPantheR_ROIStatistics | 8.558 | 0.065 | 8.670 | |
peakPantheR_loadAnnotationParamsCSV | 0.002 | 0.000 | 0.003 | |
peakPantheR_parallelAnnotation | 6.651 | 0.032 | 6.692 | |
peakPantheR_plotEICFit | 0.095 | 0.002 | 0.096 | |
peakPantheR_plotPeakwidth | 0.155 | 0.005 | 0.160 | |
peakPantheR_quickEIC | 1.781 | 0.014 | 1.795 | |
peakPantheR_singleFileSearch | 2.247 | 0.011 | 2.262 | |
peakPantheR_start_GUI | 0 | 0 | 0 | |
peakTables-peakPantheRAnnotation-method | 0.008 | 0.000 | 0.008 | |
resetAnnotation-peakPantheRAnnotation-method | 0.008 | 0.000 | 0.009 | |
resetFIR-peakPantheRAnnotation-method | 0.001 | 0.000 | 0.002 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 4.297 | 0.014 | 4.319 | |
spectraMetadata-peakPantheRAnnotation-method | 0.007 | 0.000 | 0.008 | |
spectraPaths_and_metadata_UI_helper | 0.001 | 0.000 | 0.001 | |
spectra_metadata_colourScheme_UI_helper | 0.001 | 0.000 | 0.002 | |
uROI-peakPantheRAnnotation-method | 0.007 | 0.001 | 0.007 | |
uROIExist-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.006 | |
useFIR-peakPantheRAnnotation-method | 0.007 | 0.000 | 0.008 | |
useUROI-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.006 | |