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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings MSnbase_2.37.2.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MSnbase.Rcheck’
* using R version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* current time: 2026-04-04 19:08:25 UTC
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘2.37.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Laurent Gatto <laurent.gatto@uclouvain.be>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

Uses the non-portable package: ‘mzR (>= 2.29.3)’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field should not start with the package name,
  'This package' or similar.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘missing-data.Rd’:
    \keyword{documentation, internal}
* 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 ‘MSnbase’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.7Mb
    libs   1.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Laurent Gatto <laurent.gatto@uclouvain.be> [aut, cre] (ORCID: <https://orcid.org/0000-0002-1520-2268>)
  Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] (ORCID: <https://orcid.org/0000-0002-6977-7147>)
  Sebastian Gibb <mail@sebastiangibb.de> [aut, cre] (ORCID: <https://orcid.org/0000-0001-7406-4443>)
Author field differs from that derived from Authors@R
  Author:    ‘Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker, Lieven Clement and Pascal Maas.’
  Authors@R: ‘Laurent Gatto [aut, cre] (ORCID: <https://orcid.org/0000-0002-1520-2268>), Guangchuang Yu [ctb], Samuel Wieczorek [ctb], Vasile-Cosmin Lazar [ctb], Vladislav Petyuk [ctb], Thomas Naake [ctb], Richie Cotton [ctb], Steffen Neumann [ctb], Arne Smits [ctb], Martina Fischer [ctb], Adriaan Sticker [ctb], Ludger Goeminne [ctb], Lieven Clement [ctb], Sigurdur Smarason [ctb], Miguel Cosenza-Contreras [ctb], Pascal Maas [ctb] (ORCID: <https://orcid.org/0000-0001-9379-6041>), Johannes Rainer [aut, cre] (ORCID: <https://orcid.org/0000-0002-6977-7147>), Sebastian Gibb [aut, cre] (ORCID: <https://orcid.org/0000-0001-7406-4443>)’

Maintainer field differs from that derived from Authors@R
  Maintainer: ‘Laurent Gatto <laurent.gatto@uclouvain.be>’
  Authors@R:  ‘’

* 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
':::' calls which should be '::':
  ‘S4Vectors:::makeClassinfoRowForCompactPrinting’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
  ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
  ‘MALDIquant:::.savitzkyGolay’ ‘mzR:::.hasChromatograms’
  ‘mzR:::.hasSpectra’
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'impute.Rd':
  ‘[MsCoreUtils:imputation]{MsCoreUtils::impute_matrix()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Chromatogram-class.Rd: closest
  FeaturesOfInterest-class.Rd: Versioned-class
  MIAPE-class.Rd: MIAME-class, MIAxE-class, Versioned-class
  MSnExp-class.Rd: AnnotatedDataFrame-class, phenoData, eSet-class,
    featureData, experimentData, protocolData, Versions-class,
    VersionedBiobase-class, Versioned-class, isolationWindow
  MSnProcess-class.Rd: Versioned-class
  MSnSet-class.Rd: eSet-class, ExpressionSet-class,
    AnnotatedDataFrame-class, AssayData-class, exprs, assayData,
    phenoData, featureData, experimentData, protocolData,
    Versions-class, VersionedBiobase-class, Versioned-class, impute,
    meanSdPlot, ma.plot, mva.pairs
  MSnSetList-class.Rd: AnnotatedDataFrame-class
  MSpectra.Rd: mcols, DataFrame, SimpleList
  OnDiskMSnExp-class.Rd: AnnotatedDataFrame-class, phenoData,
    featureData, experimentData, eSet-class, protocolData,
    Versions-class, VersionedBiobase-class, Versioned-class
  ProcessingStep-class.Rd: Versioned-class
  ReporterIons-class.Rd: Versioned-class
  Spectrum-class.Rd: Versioned-class
  Spectrum1-class.Rd: Versioned-class
  Spectrum2-class.Rd: Versioned-class
  combineFeatures.Rd: impute
  combineSpectra.Rd: bpparam
  extractSpectraData.Rd: DataFrame
  normToReference.Rd: exprs
  normalise-methods.Rd: vsn2
  pSet-class.Rd: eSet-class, AnnotatedDataFrame-class, phenoData,
    featureData, experimentData, protocolData, Versions-class,
    VersionedBiobase-class, Versioned-class
  plotMzDelta-methods.Rd: geom_histogram
  readMSData.Rd: AnnotatedDataFrame-class
  readMSnSet.Rd: readExpressionSet, read.AnnotatedDataFrame, read.MIAME
  readMgfData.Rd: AnnotatedDataFrame-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MSnbase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimateMzResolution,MSnExp-method
> ### Title: Estimate the m/z resolution of a spectrum
> ### Aliases: estimateMzResolution,MSnExp-method
> ###   estimateMzResolution,Spectrum-method estimateMzResolution
> 
> ### ** Examples
> 
> 
> ## Load a profile mode example file
> library(BiocParallel)
> register(SerialParam())
> library(msdata)

 IMPORTANT: msdata will be deprecated and replaced by the new
 MsDataHub package -- see https://bioconductor.org/packages/MsDataHub.
 Please open an issue at https://github.com/rformassspectrometry/MsDataHub/issues
 to inform us of any data from msdata that would need to be moved to MsDataHub.

> f <- proteomics(full.names = TRUE,
+     pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
> 
> od <- readMSData(f, mode = "onDisk")
Error in files[.hasSpecs] : invalid subscript type 'list'
Calls: readMSData
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
chromatogram-MSnExp-method 11.372  0.362  11.736
OnDiskMSnExp-class          7.016  0.108   7.165
* 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:
      ▆
   1. └─MSnbase::readMSData(f, verbose = FALSE, mode = "onDisk") at test_readMSData2.R:6:5
  ── Error ('test_readMSData2.R:67:5'): Constructor performance and test for MSn ──
  Error in `files[.hasSpecs]`: invalid subscript type 'list'
  Backtrace:
      ▆
   1. └─MSnbase::readMSData(files = mzf, centroided = TRUE, mode = "onDisk") at test_readMSData2.R:67:5
  
  [ FAIL 5 | WARN 1091 | SKIP 10 | PASS 2323 ]
  Error:
  ! Test failures.
  Warning message:
  In for (i in seq_len(n)) { :
    closing unused connection 4 (/tmp/RtmppCxYbw/file10a58b297b6257)
  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: 2 ERRORs, 4 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MSnbase.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL MSnbase
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘MSnbase’ ...
** this is package ‘MSnbase’ version ‘2.37.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function]
    8 | static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
      |             ^~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function]
    9 | static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
      |             ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
utils.c: In function ‘compar_double_dd_for_stable_asc_order’:
utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable]
   92 |   int i1, i2, ret;
      |               ^~~
utils.c: In function ‘compar_double_dd_for_stable_desc_order’:
utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable]
  107 |   int i1, i2, ret;
      |               ^~~
utils.c: In function ‘compar_double_asc_order’:
utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable]
  123 |   double d1, d2, ret;
      |                  ^~~
utils.c: In function ‘compar_double_desc_order’:
utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable]
  133 |   double d1, d2, ret;
      |                  ^~~
utils.c: At top level:
utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function]
  131 | static int compar_double_desc_order(const void *p1, const void *p2)
      |            ^~~~~~~~~~~~~~~~~~~~~~~~
utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function]
  121 | static int compar_double_asc_order(const void *p1, const void *p2)
      |            ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -shared -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-MSnbase/00new/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp”
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSnbase)

R version 4.6.0 alpha (2026-03-30 r89742)
Copyright (C) 2026 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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library("testthat")
> library("MSnbase")
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

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: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.37.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.
 Consider switching to the 'R for Mass Spectrometry'
 packages - see https://RforMassSpectrometry.org for details.


Attaching package: 'MSnbase'

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

    trimws

> setMSnbaseVerbose(FALSE)
> ## register(SerialParam()) ## see issue 205
> 
> ## Erwinia
> f <- MsDataHub::TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz()
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> tmt_erwinia_in_mem_ms1 <- readMSData(f, msLevel. = 1)
> tmt_erwinia_in_mem_ms2 <- readMSData(f, msLevel. = 2)
> tmt_erwinia_on_disk <- readMSData(f, mode = "onDisk")
> tmt_erwinia_on_disk_ms1 <- readMSData(f, msLevel. = 1, mode = "onDisk")
> tmt_erwinia_on_disk_ms2 <- readMSData(f, msLevel. = 2, mode = "onDisk")
> ## subset by rt
> tmt_im_ms1_sub <- filterRt(tmt_erwinia_in_mem_ms1, c(1200, 1250))
> tmt_im_ms2_sub <- filterRt(tmt_erwinia_in_mem_ms2, c(1200, 1250))
> tmt_od_sub <- filterRt(tmt_erwinia_on_disk, c(1200, 1250))
> tmt_od_ms1_sub <- filterRt(tmt_erwinia_on_disk_ms1, c(1200, 1250))
> tmt_od_ms2_sub <- filterRt(tmt_erwinia_on_disk_ms2, c(1200, 1250))
> 
> ## microtofq
> f <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+        system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_in_mem_ms1 <- readMSData(f, msLevel. = 1)
> microtofq_on_disk_ms1 <- readMSData(f, msLevel. = 1, mode = "onDisk")
> microtofq_on_disk <- readMSData(f, mode = "onDisk")
> 
> ## extdata mzML
> f <- dir(system.file(package = "MSnbase", dir = "extdata"),
+          full.names = TRUE, pattern = "mzXML$")
> extdata_mzXML_in_mem_ms2 <- readMSData(f, verbose = FALSE, centroided. = FALSE)
> extdata_mzXML_on_disk <- readMSData(f, centroided. = FALSE, mode = "onDisk")
> extdata_mzXML_on_disk_ms2 <- readMSData(f, msLevel. = 2, centroided. = FALSE, mode = "onDisk")
> 
> sf <- dir(system.file("sciex", package = "msdata"),
+           full.names = TRUE)
> sciex <- readMSData(sf, mode = "onDisk")
> 
> test_check("MSnbase")
Experiment data
  Experimenter name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Contact information: Laurent Gatto 
  Contact email: lg390@cam.ac.uk 
  Title: Example 'MSnExp' data set 
  URL:  
  PMIDs:  
  No abstract available.
Instrument : 
  Model: test (1) 
  Manufacturer:  
  Customisations:  
  Use 'msInfo(object)' for more MIAPE-MS information.
Experiment data
  Experimenter name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Contact information: Laurent Gatto 
  Contact email: lg390@cam.ac.uk 
  Title: Example 'MSnExp' data set 
  URL:  
  PMIDs:  
  No abstract available.
  notes:
   Note1:
First note
MIAPE-MS information:
 1. General features:
  Date stamp:  
  Contact: Laurent Gatto 
  Name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Instument model: test 
  Manufacturer:  
  Customisations:  
  Software:  
  Version:  
  Switching:  
  Param file:  
 2. Ion source
  Source:  
  Source details:  
 3. Post-source componentry
  Analyzer:  
  Analyzer details:  
  Collision gas:  
  Pressure:   bars
  Energy:  
  Detector type:  
  Sensitivity:  
Object of class "MSmap"
 Map [75, 401]
  [1]  Retention time: 30:01 - 34:58 
  [2]  M/Z: 521 - 523 (res 0.005)
Object of class "MSmap"
 Map [401, 75]
  [1]  M/Z: 521 - 523 (res 0.005)
  [2]  Retention time: 30:01 - 34:58 
Object of class "MzTab".
 Description: mzTab example file for reporting a summary report of
 quantification data quantified on the protein level
 Mode: Complete 
 Type: Quantification 
 Available data: Proteins  PSMs  
Object of class "MzTab".
 Description:
 Mode: 
 Type: 
 Available data: SmallMolecules  
Object of class "MzTab".
 Description:
 Mode: 
 Type: 
 Available data: SmallMolecules  
Instance of class 'MSnSetList' containig 3 objects.
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 3.36 Mb
- - - Spectra data - - -
 MS level(s): 1 2 
 Number of spectra: 7534 
 MSn retention times: 0:00 - 60:02 minutes
- - - Processing information - - -
Data loaded [Sat Apr  4 15:15:24 2026] 
 MSnbase version: 2.37.2 
- - - Meta data  - - -
phenoData
  rowNames: 129583763e7ece_7858
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  129583763e7ece_7858 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S7534 (7534 total)
  fvarLabels: fileIdx spIdx ... spectrum (36 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Saving _problems/test_OnDiskMSnExp2-85.R
Object of class "ReporterIons"
TMT10HCD: '10-plex TMT HCD' with 10 reporter ions
 - [126] 126.1277 +/- 0.002 (#8DD3C7)
 - [127N] 127.1248 +/- 0.002 (#FFFFB3)
 - [127C] 127.1311 +/- 0.002 (#BEBADA)
 - [128N] 128.1281 +/- 0.002 (#FB8072)
 - [128C] 128.1344 +/- 0.002 (#80B1D3)
 - [129N] 129.1315 +/- 0.002 (#FDB462)
 - [129C] 129.1378 +/- 0.002 (#B3DE69)
 - [130N] 130.1348 +/- 0.002 (#FCCDE5)
 - [130C] 130.1411 +/- 0.002 (#D9D9D9)
 - [131] 131.1382 +/- 0.002 (#BC80BD)
Object of class "Spectrum1"
 Retention time: 0:00 
 MSn level: 1 
 Total ion count: 684 
 Polarity: 1 
MSn experiment data ("MSnExp")
Object size in memory: 0.18 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 5 
 MSn retention times: 25:01 - 25:02 minutes
- - - Processing information - - -
Data loaded: Sat Apr  4 15:30:00 2026 
 MSnbase version: 2.37.2 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
  fvarLabels: spectrum
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
MSn experiment data ("MSnExp")
Object size in memory: 0.2 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 5 
 MSn retention times: 25:01 - 25:02 minutes
- - - Processing information - - -
Data loaded: Sat Apr  4 15:30:01 2026 
 MSnbase version: 2.37.2 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
  fvarLabels: spectrum
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Object of class "FeaturesOfInterest"
 Created on Sat Apr  4 15:32:13 2026 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Sat Apr  4 15:32:13 2026 
 Description:
  my description
 10 features of interest:
   P20353, P53501  ...  Q9VCK0, Q9VIU7
A collection of 1 features of interest.
A collection of 10 features of interest.
MSpectra with 3 spectra and 1 metadata column(s):
  msLevel   rtime peaksCount | id
1       2      NA          3 |  1
2       2 1.23245          4 |  2
3       1 1.23245          5 |  3
MSpectra with 3 spectra and 1 metadata column(s):
    msLevel     rtime peaksCount |        id
  <integer> <numeric>  <integer> | <integer>
1         2        NA          3 |         1
2         2   1.23245          4 |         2
3         1   1.23245          5 |         3
MSpectra with 3 spectra and 1 metadata column(s):
      msLevel     rtime peaksCount |        id
    <integer> <numeric>  <integer> | <integer>
  1         2        NA          3 |         1
  2         2   1.23245          4 |         2
  3         1   1.23245          5 |         3
Saving _problems/test_functions-MSpectra-88.R
Saving _problems/test_functions-MSpectra-115.R
reading dummyiTRAQ.mzid... DONE!
Saving _problems/test_readMSData2-6.R
Saving _problems/test_readMSData2-67.R
[ FAIL 5 | WARN 1091 | SKIP 10 | PASS 2323 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• empty test (10): 'test_MzTab.R:108:1', 'test_MzTab.R:123:1',
  'test_OnDiskMSnExp2.R:132:1', 'test_functions-Chromatogram.R:39:1',
  'test_functions-MSpectra.R:72:1', 'test_functions-plotting.R:1:1',
  'test_io.R:3:1', 'test_methods-MChromatograms.R:155:1',
  'test_readMSData2.R:51:1', 'test_readMSData2.R:80:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_OnDiskMSnExp2.R:85:5'): Default and setting centroided ─────────
Error in `files[.hasSpecs]`: invalid subscript type 'list'
Backtrace:
    ▆
 1. └─MSnbase::readMSData(f, verbose = FALSE, centroided. = NA) at test_OnDiskMSnExp2.R:85:5
── Error ('test_functions-MSpectra.R:88:5'): extractSpectraData works ──────────
Error in `(function (cond)  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "inherits(x, \"mzR\") is not TRUE", call = FUN(X[[i]], ...)), class = c("simpleError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'filterRt': inherits(x, "mzR") is not TRUE
Backtrace:
     ▆
  1. ├─ProtGenerics::filterRt(...) at test_functions-MSpectra.R:88:5
  2. ├─MSnbase::readMSData(fl, mode = "onDisk")
  3. │ └─MSnbase::hasSpectra(files)
  4. │   ├─BiocGenerics::sapply(files, mzR:::.hasSpectra)
  5. │   └─base::sapply(files, mzR:::.hasSpectra)
  6. │     └─base::lapply(X = X, FUN = FUN, ...)
  7. │       └─mzR (local) FUN(X[[i]], ...)
  8. │         └─base::stopifnot(inherits(x, "mzR"))
  9. │           └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
 10. └─base (local) `<fn>`(`<smplErrr>`)
── Error ('test_functions-MSpectra.R:115:5'): .spectra_to_spectrum_list and as,Spectra,MSpectra works ──
Error in `.local(object, ...)`: File(s)  not found
Backtrace:
    ▆
 1. ├─Spectra::Spectra(fl) at test_functions-MSpectra.R:115:5
 2. └─Spectra::Spectra(fl)
 3.   └─Spectra (local) .local(object, ...)
 4.     └─Spectra:::.create_spectra(...)
 5.       ├─ProtGenerics::backendInitialize(...)
 6.       └─Spectra::backendInitialize(...)
 7.         └─Spectra (local) .local(object, ...)
── Error ('test_readMSData2.R:6:5'): msLevel set correctly ─────────────────────
Error in `files[.hasSpecs]`: invalid subscript type 'list'
Backtrace:
    ▆
 1. └─MSnbase::readMSData(f, verbose = FALSE, mode = "onDisk") at test_readMSData2.R:6:5
── Error ('test_readMSData2.R:67:5'): Constructor performance and test for MSn ──
Error in `files[.hasSpecs]`: invalid subscript type 'list'
Backtrace:
    ▆
 1. └─MSnbase::readMSData(files = mzf, centroided = TRUE, mode = "onDisk") at test_readMSData2.R:67:5

[ FAIL 5 | WARN 1091 | SKIP 10 | PASS 2323 ]
Error:
! Test failures.
Warning message:
In for (i in seq_len(n)) { :
  closing unused connection 4 (/tmp/RtmppCxYbw/file10a58b297b6257)
Execution halted