Arnaud Wolfer
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/peakPantheR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 89aef90 |
| git_last_commit_date: 2024-10-29 10:40:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:07 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1522/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.20.0 (landing page) Arnaud Wolfer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | ERROR | OK | |||||||||
|
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: 1.20.0 |
| 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_1.20.0.tar.gz |
| StartedAt: 2025-01-01 04:11:55 -0500 (Wed, 01 Jan 2025) |
| EndedAt: 2025-01-01 04:36:12 -0500 (Wed, 01 Jan 2025) |
| EllapsedTime: 1456.2 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/peakPantheR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘1.20.0’
* 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 24.541 0.201 24.875
peakPantheR_parallelAnnotation 19.095 0.106 19.215
outputAnnotationDiagnostic-peakPantheRAnnotation-method 18.442 0.106 18.590
outputAnnotationResult-peakPantheRAnnotation-method 18.289 0.082 18.374
EICs-peakPantheRAnnotation-method 14.046 0.531 14.598
retentionTimeCorrection-peakPantheRAnnotation-method 12.501 0.061 12.571
peakPantheR_singleFileSearch 6.398 0.037 6.436
peakPantheR_quickEIC 5.350 0.033 5.384
* 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/tmp/RtmpospHzu/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/private/tmp/RtmpospHzu/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/private/tmp/RtmpospHzu/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/private/tmp/RtmpospHzu/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.4-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-3.20-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/4.4-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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 1.20.0
>
> test_check("peakPantheR")
2025-01-01 04:21:27.898 R[98129:110024985] XType: Using static font registry.
2025-01-01 04:21:43.426 R[5008:110040670] XType: Using static font registry.
2025-01-01 04:21:53.067 R[5125:110041076] XType: Using static font registry.
2025-01-01 04:26:35.978 R[7603:110048244] 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$mzMax fo
x[3]: r ROI #4\n"
y[3]: "Fit of ROI #3 is unsuccessful (apex residuals is 0.45 of max fit intensit
y[3]: y, max intensity residuals is 0.46 of max fit intensity)\n"
x[4]: "Found 4/4 features in 0.03 secs\n"
y[4]: "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/
y[4]: mzMax calculation, approximate mz and returning ROI$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: 19.51 secs\n"
y[21]: "----------------\n"
x[22]: "Annotation parameters saved at /private/tmp/RtmpospHzu/IS_search/annotati
x[22]: onParameters_summary.csv\n"
y[22]: " 0 failure(s)\n"
x[23]: " Compound 1/4 diagnostic plot saved at /private/tmp/RtmpospHzu/IS_search
x[23]: /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: 19.55 secs\n"
y[12]: "----------------\n"
x[13]: "IS mean RT saved at /private/tmp/RtmpospHzu/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/tmp/RtmpospHzu/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/private/tmp/RtmpospHzu/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/private/tmp/RtmpospHzu/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/private/tmp/RtmpospHzu/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
Execution halted
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 14.046 | 0.531 | 14.598 | |
| FIR-peakPantheRAnnotation-method | 0.065 | 0.003 | 0.068 | |
| ROI-peakPantheRAnnotation-method | 0.055 | 0.003 | 0.058 | |
| TIC-peakPantheRAnnotation-method | 0.054 | 0.003 | 0.057 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.057 | 0.004 | 0.061 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.064 | 0.004 | 0.068 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.060 | 0.004 | 0.064 | |
| annotationTable-peakPantheRAnnotation-method | 0.065 | 0.004 | 0.069 | |
| annotation_diagnostic_multiplot_UI_helper | 0.124 | 0.006 | 0.130 | |
| annotation_fit_summary_UI_helper | 0.008 | 0.000 | 0.008 | |
| annotation_showMethod_UI_helper | 0.004 | 0.000 | 0.004 | |
| annotation_showText_UI_helper | 0.001 | 0.000 | 0.001 | |
| cpdID-peakPantheRAnnotation-method | 0.061 | 0.004 | 0.065 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.064 | 0.004 | 0.067 | |
| cpdName-peakPantheRAnnotation-method | 0.064 | 0.004 | 0.067 | |
| dataPoints-peakPantheRAnnotation-method | 0.065 | 0.004 | 0.070 | |
| filename-peakPantheRAnnotation-method | 0.055 | 0.004 | 0.059 | |
| filepath-peakPantheRAnnotation-method | 0.059 | 0.004 | 0.063 | |
| initialise_annotation_from_files_UI_helper | 0.013 | 0.001 | 0.015 | |
| isAnnotated-peakPantheRAnnotation-method | 0.061 | 0.004 | 0.065 | |
| load_annotation_from_file_UI_helper | 0.007 | 0.001 | 0.007 | |
| nbCompounds-peakPantheRAnnotation-method | 0.054 | 0.004 | 0.058 | |
| nbSamples-peakPantheRAnnotation-method | 0.054 | 0.004 | 0.057 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 18.442 | 0.106 | 18.590 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.005 | 0.001 | 0.006 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.022 | 0.001 | 0.023 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 18.289 | 0.082 | 18.374 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.006 | 0.000 | 0.006 | |
| peakFit-peakPantheRAnnotation-method | 0.057 | 0.004 | 0.062 | |
| peakPantheRAnnotation | 0.073 | 0.005 | 0.078 | |
| peakPantheR_ROIStatistics | 24.541 | 0.201 | 24.875 | |
| peakPantheR_loadAnnotationParamsCSV | 0.007 | 0.001 | 0.008 | |
| peakPantheR_parallelAnnotation | 19.095 | 0.106 | 19.215 | |
| peakPantheR_plotEICFit | 0.314 | 0.004 | 0.320 | |
| peakPantheR_plotPeakwidth | 0.513 | 0.008 | 0.522 | |
| peakPantheR_quickEIC | 5.350 | 0.033 | 5.384 | |
| peakPantheR_singleFileSearch | 6.398 | 0.037 | 6.436 | |
| peakPantheR_start_GUI | 0.000 | 0.001 | 0.001 | |
| peakTables-peakPantheRAnnotation-method | 0.057 | 0.003 | 0.060 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.068 | 0.004 | 0.072 | |
| resetFIR-peakPantheRAnnotation-method | 0.005 | 0.001 | 0.005 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 12.501 | 0.061 | 12.571 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.090 | 0.005 | 0.105 | |
| spectraPaths_and_metadata_UI_helper | 0.003 | 0.001 | 0.004 | |
| spectra_metadata_colourScheme_UI_helper | 0.006 | 0.000 | 0.007 | |
| uROI-peakPantheRAnnotation-method | 0.065 | 0.004 | 0.071 | |
| uROIExist-peakPantheRAnnotation-method | 0.056 | 0.003 | 0.058 | |
| useFIR-peakPantheRAnnotation-method | 0.055 | 0.003 | 0.058 | |
| useUROI-peakPantheRAnnotation-method | 0.056 | 0.002 | 0.059 | |