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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R 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 1514/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.21.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: devel
git_last_commit: 4d6e977
git_last_commit_date: 2024-10-29 10:40:22 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for peakPantheR on kjohnson3

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method4.4720.1404.630
FIR-peakPantheRAnnotation-method0.0080.0000.009
ROI-peakPantheRAnnotation-method0.0060.0010.007
TIC-peakPantheRAnnotation-method0.0060.0000.006
acquisitionTime-peakPantheRAnnotation-method0.0060.0010.007
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0060.0010.006
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0060.0000.006
annotationTable-peakPantheRAnnotation-method0.0050.0010.007
annotation_diagnostic_multiplot_UI_helper0.0490.0020.052
annotation_fit_summary_UI_helper0.0020.0000.002
annotation_showMethod_UI_helper0.0010.0000.002
annotation_showText_UI_helper0.0010.0010.000
cpdID-peakPantheRAnnotation-method0.0060.0000.008
cpdMetadata-peakPantheRAnnotation-method0.0060.0000.006
cpdName-peakPantheRAnnotation-method0.0050.0010.005
dataPoints-peakPantheRAnnotation-method0.0050.0000.006
filename-peakPantheRAnnotation-method0.0050.0010.005
filepath-peakPantheRAnnotation-method0.0050.0000.005
initialise_annotation_from_files_UI_helper0.0040.0000.004
isAnnotated-peakPantheRAnnotation-method0.0060.0010.006
load_annotation_from_file_UI_helper0.0020.0000.002
nbCompounds-peakPantheRAnnotation-method0.0050.0010.006
nbSamples-peakPantheRAnnotation-method0.0050.0000.006
outputAnnotationDiagnostic-peakPantheRAnnotation-method6.5710.0266.656
outputAnnotationFeatureMetadata_UI_helper0.0020.0000.002
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0070.0000.008
outputAnnotationResult-peakPantheRAnnotation-method6.3190.0196.357
outputAnnotationSpectraMetadata_UI_helper0.0020.0000.002
peakFit-peakPantheRAnnotation-method0.0070.0010.008
peakPantheRAnnotation0.0090.0000.010
peakPantheR_ROIStatistics8.5580.0658.670
peakPantheR_loadAnnotationParamsCSV0.0020.0000.003
peakPantheR_parallelAnnotation6.6510.0326.692
peakPantheR_plotEICFit0.0950.0020.096
peakPantheR_plotPeakwidth0.1550.0050.160
peakPantheR_quickEIC1.7810.0141.795
peakPantheR_singleFileSearch2.2470.0112.262
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.0080.0000.008
resetAnnotation-peakPantheRAnnotation-method0.0080.0000.009
resetFIR-peakPantheRAnnotation-method0.0010.0000.002
retentionTimeCorrection-peakPantheRAnnotation-method4.2970.0144.319
spectraMetadata-peakPantheRAnnotation-method0.0070.0000.008
spectraPaths_and_metadata_UI_helper0.0010.0000.001
spectra_metadata_colourScheme_UI_helper0.0010.0000.002
uROI-peakPantheRAnnotation-method0.0070.0010.007
uROIExist-peakPantheRAnnotation-method0.0060.0010.006
useFIR-peakPantheRAnnotation-method0.0070.0000.008
useUROI-peakPantheRAnnotation-method0.0060.0010.006