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This page was generated on 2024-04-18 11:32:15 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1520/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.16.1 (landing page) Arnaud Wolfer
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the peakPantheR package: - 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: 1.16.1 |
| 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_1.16.1.tar.gz |
| StartedAt: 2024-04-17 22:43:49 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 23:05:13 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 1283.4 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_1.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/peakPantheR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.16.1’
* 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 R 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 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 24.631 0.259 25.545
peakPantheR_parallelAnnotation 18.735 0.116 18.954
outputAnnotationDiagnostic-peakPantheRAnnotation-method 18.027 0.125 18.406
outputAnnotationResult-peakPantheRAnnotation-method 17.820 0.089 17.985
EICs-peakPantheRAnnotation-method 14.732 0.481 15.333
retentionTimeCorrection-peakPantheRAnnotation-method 12.705 0.067 12.837
peakPantheR_singleFileSearch 6.437 0.053 6.523
* 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/RtmptyKPvt/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/private/tmp/RtmptyKPvt/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/private/tmp/RtmptyKPvt/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/private/tmp/RtmptyKPvt/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc-mac-arm64/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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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 1.16.1
>
> test_check("peakPantheR")
2024-04-17 22:53:14.539 R[50115:453955219] XType: Using static font registry.
2024-04-17 22:53:31.517 R[54908:453967037] XType: Using static font registry.
2024-04-17 22:53:41.685 R[54951:453967263] XType: Using static font registry.
2024-04-17 22:57:50.688 R[57893:453974585] XType: Using static font registry.
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 1447 ]
══ 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$mzMax fo
x[3]: r ROI #4\n"
y[3]: "Fit of ROI #3 is unsuccessful (apex residuals is 0.45 of max fit intensit
y[3]: y, max intensity residuals is 0.46 of max fit intensity)\n"
x[4]: "Found 4/4 features in 0.04 secs\n"
y[4]: "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/
y[4]: mzMax calculation, approximate mz and returning ROI$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: 19.64 secs\n"
y[21]: "----------------\n"
x[22]: "Annotation parameters saved at /private/tmp/RtmptyKPvt/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/RtmptyKPvt/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: 19.33 secs\n"
y[12]: "----------------\n"
x[13]: "IS mean RT saved at /private/tmp/RtmptyKPvt/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 1447 ]
Error: Test failures
In addition: Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 10 (/private/tmp/RtmptyKPvt/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/private/tmp/RtmptyKPvt/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/private/tmp/RtmptyKPvt/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/private/tmp/RtmptyKPvt/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
Execution halted
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 14.732 | 0.481 | 15.333 | |
| FIR-peakPantheRAnnotation-method | 0.202 | 0.017 | 0.219 | |
| ROI-peakPantheRAnnotation-method | 0.202 | 0.017 | 0.219 | |
| TIC-peakPantheRAnnotation-method | 0.190 | 0.016 | 0.206 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.238 | 0.018 | 0.257 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.184 | 0.015 | 0.199 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.187 | 0.014 | 0.200 | |
| annotationTable-peakPantheRAnnotation-method | 0.200 | 0.015 | 0.217 | |
| annotation_diagnostic_multiplot_UI_helper | 0.138 | 0.014 | 0.159 | |
| annotation_fit_summary_UI_helper | 0.009 | 0.001 | 0.010 | |
| annotation_showMethod_UI_helper | 0.003 | 0.001 | 0.004 | |
| annotation_showText_UI_helper | 0.000 | 0.001 | 0.001 | |
| cpdID-peakPantheRAnnotation-method | 0.207 | 0.017 | 0.225 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.224 | 0.024 | 0.248 | |
| cpdName-peakPantheRAnnotation-method | 0.185 | 0.011 | 0.196 | |
| dataPoints-peakPantheRAnnotation-method | 0.187 | 0.012 | 0.199 | |
| filename-peakPantheRAnnotation-method | 0.182 | 0.012 | 0.194 | |
| filepath-peakPantheRAnnotation-method | 0.197 | 0.012 | 0.212 | |
| initialise_annotation_from_files_UI_helper | 0.013 | 0.001 | 0.014 | |
| isAnnotated-peakPantheRAnnotation-method | 0.197 | 0.012 | 0.208 | |
| load_annotation_from_file_UI_helper | 0.006 | 0.001 | 0.008 | |
| nbCompounds-peakPantheRAnnotation-method | 0.212 | 0.013 | 0.226 | |
| nbSamples-peakPantheRAnnotation-method | 0.200 | 0.012 | 0.213 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 18.027 | 0.125 | 18.406 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.005 | 0.001 | 0.006 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.023 | 0.002 | 0.025 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 17.820 | 0.089 | 17.985 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.006 | 0.000 | 0.006 | |
| peakFit-peakPantheRAnnotation-method | 0.217 | 0.013 | 0.232 | |
| peakPantheRAnnotation | 0.237 | 0.014 | 0.252 | |
| peakPantheR_ROIStatistics | 24.631 | 0.259 | 25.545 | |
| peakPantheR_loadAnnotationParamsCSV | 0.006 | 0.001 | 0.007 | |
| peakPantheR_parallelAnnotation | 18.735 | 0.116 | 18.954 | |
| peakPantheR_plotEICFit | 0.301 | 0.004 | 0.306 | |
| peakPantheR_plotPeakwidth | 0.521 | 0.014 | 0.536 | |
| peakPantheR_singleFileSearch | 6.437 | 0.053 | 6.523 | |
| peakPantheR_start_GUI | 0.001 | 0.000 | 0.000 | |
| peakTables-peakPantheRAnnotation-method | 0.233 | 0.013 | 0.255 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.231 | 0.012 | 0.246 | |
| resetFIR-peakPantheRAnnotation-method | 0.006 | 0.000 | 0.006 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 12.705 | 0.067 | 12.837 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.218 | 0.013 | 0.233 | |
| spectraPaths_and_metadata_UI_helper | 0.003 | 0.001 | 0.004 | |
| spectra_metadata_colourScheme_UI_helper | 0.005 | 0.001 | 0.005 | |
| uROI-peakPantheRAnnotation-method | 0.224 | 0.013 | 0.240 | |
| uROIExist-peakPantheRAnnotation-method | 0.225 | 0.013 | 0.247 | |
| useFIR-peakPantheRAnnotation-method | 0.228 | 0.012 | 0.242 | |
| useUROI-peakPantheRAnnotation-method | 0.218 | 0.012 | 0.233 | |