| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 1550/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.23.0 (landing page) Arnaud Wolfer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.23.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings peakPantheR_1.23.0.tar.gz |
| StartedAt: 2025-09-20 02:49:37 -0400 (Sat, 20 Sep 2025) |
| EndedAt: 2025-09-20 03:14:23 -0400 (Sat, 20 Sep 2025) |
| EllapsedTime: 1486.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: peakPantheR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings peakPantheR_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/peakPantheR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.23.0’
* 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 loading without being on the library search path ... 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 23.270 0.232 23.511
peakPantheR_parallelAnnotation 16.358 0.061 16.420
outputAnnotationResult-peakPantheRAnnotation-method 15.787 0.061 15.850
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.572 0.152 15.774
EICs-peakPantheRAnnotation-method 11.577 0.580 12.171
retentionTimeCorrection-peakPantheRAnnotation-method 9.861 0.040 9.901
peakPantheR_singleFileSearch 5.369 0.021 5.390
* 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 (/tmp/RtmpGIEBIU/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/tmp/RtmpGIEBIU/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/tmp/RtmpGIEBIU/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/tmp/RtmpGIEBIU/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/home/biocbuild/bbs-3.22-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/home/biocbuild/bbs-3.22-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.22-bioc/meat/peakPantheR.Rcheck/00check.log’
for details.
peakPantheR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘peakPantheR’ ... ** this is package ‘peakPantheR’ version ‘1.23.0’ ** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 1.23.0
>
> test_check("peakPantheR")
[ FAIL 13 | WARN 1 | SKIP 0 | PASS 1459 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_peakPantheRAnnotation_retentionTimeCorrection-method.R:176:3'): rt correction plot (uROI) ──
<subscriptOutOfBoundsError/error/condition>
Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_peakPantheRAnnotation_retentionTimeCorrection-method.R:176:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─resultCorrected$result$plot[[1]]
5. └─ggplot2 (local) `[[.ggplot2::gg`(resultCorrected$result$plot, 1)
── Failure ('test_peakPantheR_plotPeakwidth.R:23:3'): plot 3 samples, no color ──
result_3splNoColNoRot$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:50:3'): plot 3 samples, no color, rotate axis ──
result_3splNoColRot$labels$y not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:75:3'): plot 4 samples with color ──
result_4splWithColNoRot$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:102:3'): plot 4 samples with color, rotate axis ──
result_4splWithColRot$labels$y not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:134:3'): sampleColour length warning, peakwidth and rotate and input order message ──
result_plotColourWarning$result$labels$y not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:171:3'): missing widthMin, no peakwidth plot ──
result_plotNoWidthMin$result$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:190:3'): missing widthMax, no peakwidth plot ──
result_plotNoWidthMax$result$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:209:3'): NA in acquisition time, revert to input order plot ──
result_plotFallBackNAAcqu$result$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_plotHistogram.R:33:3'): histogram and density, with NA in input ──
result_histoAndDensity$labels$y not equal to "density".
target is NULL, current is character
── Failure ('test_plotHistogram.R:38:3'): histogram and density, with NA in input ──
result_message$messages not equal to `expected_message`.
1/1 mismatches
x[1]: "`stat_bin()` using `bins = 30`. Pick better value `binwidth`."
y[1]: "`stat_bin()` using `bins = 30`. Pick better value with `binwidth`."
── Failure ('test_plotHistogram.R:51:3'): histogram without density ────────────
result_histoNoDensity$labels$y[1] not equal to "count".
target is NULL, current is character
── Failure ('test_plotHistogram.R:72:3'): histogram and density with modified ... (bins) ──
result_histoChangeBins$labels$y not equal to "density".
target is NULL, current is character
[ FAIL 13 | WARN 1 | SKIP 0 | PASS 1459 ]
Error: Test failures
In addition: Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 10 (/tmp/RtmpGIEBIU/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/tmp/RtmpGIEBIU/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/tmp/RtmpGIEBIU/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/tmp/RtmpGIEBIU/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/home/biocbuild/bbs-3.22-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/home/biocbuild/bbs-3.22-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
Execution halted
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 11.577 | 0.580 | 12.171 | |
| FIR-peakPantheRAnnotation-method | 0.025 | 0.001 | 0.026 | |
| ROI-peakPantheRAnnotation-method | 0.020 | 0.000 | 0.021 | |
| TIC-peakPantheRAnnotation-method | 0.020 | 0.000 | 0.019 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.017 | 0.003 | 0.020 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.019 | 0.001 | 0.020 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.013 | 0.004 | 0.018 | |
| annotationTable-peakPantheRAnnotation-method | 0.016 | 0.003 | 0.019 | |
| annotation_diagnostic_multiplot_UI_helper | 0.149 | 0.031 | 0.179 | |
| annotation_fit_summary_UI_helper | 0.009 | 0.000 | 0.008 | |
| annotation_showMethod_UI_helper | 0.003 | 0.001 | 0.004 | |
| annotation_showText_UI_helper | 0.000 | 0.000 | 0.001 | |
| cpdID-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.016 | 0.002 | 0.018 | |
| cpdName-peakPantheRAnnotation-method | 0.016 | 0.003 | 0.018 | |
| dataPoints-peakPantheRAnnotation-method | 0.017 | 0.001 | 0.017 | |
| filename-peakPantheRAnnotation-method | 0.016 | 0.002 | 0.018 | |
| filepath-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.018 | |
| initialise_annotation_from_files_UI_helper | 0.009 | 0.003 | 0.013 | |
| isAnnotated-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |
| load_annotation_from_file_UI_helper | 0.005 | 0.002 | 0.007 | |
| nbCompounds-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.018 | |
| nbSamples-peakPantheRAnnotation-method | 0.016 | 0.004 | 0.018 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 15.572 | 0.152 | 15.774 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.005 | 0.001 | 0.004 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.021 | 0.000 | 0.021 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 15.787 | 0.061 | 15.850 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.005 | 0.000 | 0.005 | |
| peakFit-peakPantheRAnnotation-method | 0.018 | 0.000 | 0.017 | |
| peakPantheRAnnotation | 0.023 | 0.000 | 0.022 | |
| peakPantheR_ROIStatistics | 23.270 | 0.232 | 23.511 | |
| peakPantheR_loadAnnotationParamsCSV | 0.005 | 0.001 | 0.006 | |
| peakPantheR_parallelAnnotation | 16.358 | 0.061 | 16.420 | |
| peakPantheR_plotEICFit | 0.488 | 0.002 | 0.490 | |
| peakPantheR_plotPeakwidth | 0.881 | 0.000 | 0.881 | |
| peakPantheR_quickEIC | 4.838 | 0.025 | 4.864 | |
| peakPantheR_singleFileSearch | 5.369 | 0.021 | 5.390 | |
| peakPantheR_start_GUI | 0 | 0 | 0 | |
| peakTables-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.018 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.023 | 0.000 | 0.022 | |
| resetFIR-peakPantheRAnnotation-method | 0.004 | 0.000 | 0.004 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 9.861 | 0.040 | 9.901 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |
| spectraPaths_and_metadata_UI_helper | 0.002 | 0.000 | 0.002 | |
| spectra_metadata_colourScheme_UI_helper | 0.005 | 0.000 | 0.004 | |
| uROI-peakPantheRAnnotation-method | 0.019 | 0.000 | 0.018 | |
| uROIExist-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |
| useFIR-peakPantheRAnnotation-method | 0.016 | 0.000 | 0.017 | |
| useUROI-peakPantheRAnnotation-method | 0.015 | 0.001 | 0.016 | |