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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsQuality_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsQuality.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘1.6.0’
* 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 ‘MsQuality’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
calculateMetrics                 7.195  0.779   7.794
calculateMetricsFromMsExperiment 6.532  1.342   4.362
calculateMetricsFromSpectra      4.619  0.993   3.803
* 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:
  metrics_msexp_wrapper[[2]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
  1/1 mismatches
  x[1]: "obsolete TIC quarters RT fraction"
  y[1]: "TIC quarters RT fraction"
  ── Failure ('test_function_calculateMetrics_from_Spectra.R:1349:5'): calculateMetrics, format = 'mzQC'. ──
  metrics_msexp_wrapper[[2]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
  1/1 mismatches
  x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
  x[1]: es divided by retention time duration.\" [PSI:MS]"
  y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
  y[1]:  by retention time duration.\" [PSI:MS]"
  
  [ FAIL 16 | WARN 0 | SKIP 0 | PASS 850 ]
  Error: Test failures
  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-3.20-bioc/meat/MsQuality.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsQuality
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MsQuality’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (MsQuality)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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("MsQuality")
> library("Spectra")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
> library("MsExperiment")
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth

> library("msdata")
> library("S4Vectors")
> 
> test_check("MsQuality")
trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
Content type 'application/json; charset=utf-8' length 7369 bytes
==================================================
downloaded 7369 bytes

trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.188/psi-ms.obo'
Content type 'application/octet-stream' length 1007520 bytes (983 KB)
==================================================
downloaded 983 KB

[ FAIL 16 | WARN 0 | SKIP 0 | PASS 850 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_function_calculateMetrics_from_Spectra.R:694:5'): calculateMetricsFromSpectra, format = 'mzQC'. ──
metrics_spectra[[1]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:697:5'): calculateMetricsFromSpectra, format = 'mzQC'. ──
metrics_spectra[[1]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"
── Failure ('test_function_calculateMetrics_from_Spectra.R:709:5'): calculateMetricsFromSpectra, format = 'mzQC'. ──
metrics_spectra[[2]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:712:5'): calculateMetricsFromSpectra, format = 'mzQC'. ──
metrics_spectra[[2]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"
── Failure ('test_function_calculateMetrics_from_Spectra.R:923:5'): calculateMetricsFromMsExperiment, format = 'mzQC'. ──
metrics_msexp[[1]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:926:5'): calculateMetricsFromMsExperiment, format = 'mzQC'. ──
metrics_msexp[[1]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"
── Failure ('test_function_calculateMetrics_from_Spectra.R:938:5'): calculateMetricsFromMsExperiment, format = 'mzQC'. ──
metrics_msexp[[2]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:941:5'): calculateMetricsFromMsExperiment, format = 'mzQC'. ──
metrics_msexp[[2]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1134:5'): calculateMetrics, format = 'mzQC'. ──
metrics_spectra_wrapper[[1]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1137:5'): calculateMetrics, format = 'mzQC'. ──
metrics_spectra_wrapper[[1]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1149:5'): calculateMetrics, format = 'mzQC'. ──
metrics_spectra_wrapper[[2]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1152:5'): calculateMetrics, format = 'mzQC'. ──
metrics_spectra_wrapper[[2]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1331:5'): calculateMetrics, format = 'mzQC'. ──
metrics_msexp_wrapper[[1]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1334:5'): calculateMetrics, format = 'mzQC'. ──
metrics_msexp_wrapper[[1]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1346:5'): calculateMetrics, format = 'mzQC'. ──
metrics_msexp_wrapper[[2]]$runQualities[[1]]$qualityMetrics[[2]]$name not equal to "TIC quarters RT fraction".
1/1 mismatches
x[1]: "obsolete TIC quarters RT fraction"
y[1]: "TIC quarters RT fraction"
── Failure ('test_function_calculateMetrics_from_Spectra.R:1349:5'): calculateMetrics, format = 'mzQC'. ──
metrics_msexp_wrapper[[2]]$runQualities[[1]]$qualityMetrics[[2]]$description not equal to "\"The interval when the respective quarter of the TIC accumulates divided by retention time duration.\" [PSI:MS]".
1/1 mismatches
x[1]: "\"OBSOLETE. The interval when the respective quarter of the TIC accumulat
x[1]: es divided by retention time duration.\" [PSI:MS]"
y[1]: "\"The interval when the respective quarter of the TIC accumulates divided
y[1]:  by retention time duration.\" [PSI:MS]"

[ FAIL 16 | WARN 0 | SKIP 0 | PASS 850 ]
Error: Test failures
Execution halted