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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings peakPantheR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/peakPantheR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.18.0’
* 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                               25.057  0.288  25.402
peakPantheR_parallelAnnotation                          18.603  0.148  18.781
outputAnnotationDiagnostic-peakPantheRAnnotation-method 18.051  0.292  18.432
outputAnnotationResult-peakPantheRAnnotation-method     17.678  0.183  17.883
EICs-peakPantheRAnnotation-method                       15.366  0.842  16.265
retentionTimeCorrection-peakPantheRAnnotation-method    12.391  0.080  12.496
peakPantheR_singleFileSearch                             6.335  0.048   6.395
peakPantheR_quickEIC                                     5.380  0.008   5.397
* 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 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
  2: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 9 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
  3: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 8 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
  4: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 7 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
  5: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 6 (/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/peakPantheR/extdata/test_fakemzML.mzML)
  6: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 5 (/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/peakPantheR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL peakPantheR
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 1.18.0 

> 
> test_check("peakPantheR")
[ 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 0.05 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: 19.13 secs\n"
y[21]: "----------------\n"

x[22]: "Annotation parameters saved at /home/biocbuild/tmp/RtmppfHijy/IS_search/a
x[22]: nnotationParameters_summary.csv\n"
y[22]: "  0 failure(s)\n"

x[23]: "  Compound 1/4 diagnostic plot saved at /home/biocbuild/tmp/RtmppfHijy/IS
x[23]: _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: 18.96 secs\n"
y[12]: "----------------\n"

x[13]: "IS mean RT saved at /home/biocbuild/tmp/RtmppfHijy/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 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/home/biocbuild/tmp/RtmppfHijy/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/peakPantheR/extdata/test_fakemzML.mzML)
Execution halted