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This page was generated on 2024-03-28 11:32:27 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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: 2024-03-27 22:06:05 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 22:27:20 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 1274.4 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 24.052 0.226 24.302 peakPantheR_parallelAnnotation 18.802 0.135 19.011 outputAnnotationResult-peakPantheRAnnotation-method 18.019 0.106 18.495 outputAnnotationDiagnostic-peakPantheRAnnotation-method 17.913 0.094 18.045 EICs-peakPantheRAnnotation-method 14.641 0.455 15.177 retentionTimeCorrection-peakPantheRAnnotation-method 11.989 0.063 12.109 peakPantheR_singleFileSearch 6.203 0.043 6.285 * 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/RtmpzgckUK/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (/private/tmp/RtmpzgckUK/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/private/tmp/RtmpzgckUK/notValidXML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/private/tmp/RtmpzgckUK/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") 2024-03-27 22:15:26.361 R[70181:398052107] XType: Using static font registry. 2024-03-27 22:15:40.968 R[74722:398063785] XType: Using static font registry. 2024-03-27 22:15:50.308 R[74770:398063952] XType: Using static font registry. 2024-03-27 22:19:54.223 R[78278:398072166] 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: 19.52 secs\n" y[21]: "----------------\n" x[22]: "Annotation parameters saved at /private/tmp/RtmpzgckUK/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/RtmpzgckUK/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: 19.96 secs\n" y[12]: "----------------\n" x[13]: "IS mean RT saved at /private/tmp/RtmpzgckUK/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/RtmpzgckUK/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (/private/tmp/RtmpzgckUK/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/private/tmp/RtmpzgckUK/notValidXML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/private/tmp/RtmpzgckUK/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 | 14.641 | 0.455 | 15.177 | |
FIR-peakPantheRAnnotation-method | 0.213 | 0.016 | 0.230 | |
ROI-peakPantheRAnnotation-method | 0.210 | 0.015 | 0.226 | |
TIC-peakPantheRAnnotation-method | 0.192 | 0.016 | 0.208 | |
acquisitionTime-peakPantheRAnnotation-method | 0.202 | 0.016 | 0.217 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.206 | 0.017 | 0.226 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.198 | 0.016 | 0.214 | |
annotationTable-peakPantheRAnnotation-method | 0.205 | 0.017 | 0.223 | |
annotation_diagnostic_multiplot_UI_helper | 0.139 | 0.014 | 0.154 | |
annotation_fit_summary_UI_helper | 0.008 | 0.001 | 0.009 | |
annotation_showMethod_UI_helper | 0.004 | 0.001 | 0.005 | |
annotation_showText_UI_helper | 0.001 | 0.001 | 0.001 | |
cpdID-peakPantheRAnnotation-method | 0.237 | 0.018 | 0.255 | |
cpdMetadata-peakPantheRAnnotation-method | 0.218 | 0.018 | 0.236 | |
cpdName-peakPantheRAnnotation-method | 0.195 | 0.012 | 0.209 | |
dataPoints-peakPantheRAnnotation-method | 0.197 | 0.013 | 0.210 | |
filename-peakPantheRAnnotation-method | 0.205 | 0.013 | 0.218 | |
filepath-peakPantheRAnnotation-method | 0.198 | 0.013 | 0.210 | |
initialise_annotation_from_files_UI_helper | 0.013 | 0.001 | 0.014 | |
isAnnotated-peakPantheRAnnotation-method | 0.206 | 0.012 | 0.218 | |
load_annotation_from_file_UI_helper | 0.008 | 0.001 | 0.010 | |
nbCompounds-peakPantheRAnnotation-method | 0.195 | 0.013 | 0.212 | |
nbSamples-peakPantheRAnnotation-method | 0.198 | 0.013 | 0.212 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 17.913 | 0.094 | 18.045 | |
outputAnnotationFeatureMetadata_UI_helper | 0.006 | 0.001 | 0.007 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.022 | 0.002 | 0.024 | |
outputAnnotationResult-peakPantheRAnnotation-method | 18.019 | 0.106 | 18.495 | |
outputAnnotationSpectraMetadata_UI_helper | 0.006 | 0.000 | 0.006 | |
peakFit-peakPantheRAnnotation-method | 0.209 | 0.013 | 0.226 | |
peakPantheRAnnotation | 0.221 | 0.013 | 0.234 | |
peakPantheR_ROIStatistics | 24.052 | 0.226 | 24.302 | |
peakPantheR_loadAnnotationParamsCSV | 0.007 | 0.002 | 0.009 | |
peakPantheR_parallelAnnotation | 18.802 | 0.135 | 19.011 | |
peakPantheR_plotEICFit | 0.302 | 0.004 | 0.307 | |
peakPantheR_plotPeakwidth | 0.519 | 0.016 | 0.536 | |
peakPantheR_singleFileSearch | 6.203 | 0.043 | 6.285 | |
peakPantheR_start_GUI | 0 | 0 | 0 | |
peakTables-peakPantheRAnnotation-method | 0.187 | 0.009 | 0.196 | |
resetAnnotation-peakPantheRAnnotation-method | 0.167 | 0.009 | 0.177 | |
resetFIR-peakPantheRAnnotation-method | 0.005 | 0.001 | 0.005 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 11.989 | 0.063 | 12.109 | |
spectraMetadata-peakPantheRAnnotation-method | 0.224 | 0.013 | 0.240 | |
spectraPaths_and_metadata_UI_helper | 0.003 | 0.001 | 0.005 | |
spectra_metadata_colourScheme_UI_helper | 0.006 | 0.000 | 0.006 | |
uROI-peakPantheRAnnotation-method | 0.215 | 0.012 | 0.228 | |
uROIExist-peakPantheRAnnotation-method | 0.215 | 0.012 | 0.229 | |
useFIR-peakPantheRAnnotation-method | 0.212 | 0.012 | 0.225 | |
useUROI-peakPantheRAnnotation-method | 0.218 | 0.013 | 0.232 | |