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This page was generated on 2024-02-22 11:36:07 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1336/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.28.1  (landing page)
Laurent Gatto
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/MSnbase
git_branch: RELEASE_3_18
git_last_commit: 6329ed35
git_last_commit_date: 2023-11-06 01:58:23 -0500 (Mon, 06 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MSnbase on nebbiolo2


To the developers/maintainers of the MSnbase package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnbase.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.

raw results


Summary

Package: MSnbase
Version: 2.28.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSnbase_2.28.1.tar.gz
StartedAt: 2024-02-22 00:20:41 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 00:34:28 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 827.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MSnbase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSnbase_2.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSnbase.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘2.28.1’
* 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 ‘MSnbase’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.9Mb
    libs   1.1Mb
* 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] (<https://orcid.org/0000-0002-1520-2268>)
  Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] (<https://orcid.org/0000-0002-6977-7147>)
  Sebastian Gibb <mail@sebastiangibb.de> [aut, cre] (<https://orcid.org/0000-0001-7406-4443>)
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
chromatogram-MSnExp-method 11.207  0.820  12.028
MSnSet-class                8.873  0.432   9.304
OnDiskMSnExp-class          7.484  0.244   7.748
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘v01-MSnbase-demo.Rmd’ using ‘UTF-8’... OK
  ‘v02-MSnbase-io.Rmd’ using ‘UTF-8’... OK
  ‘v03-MSnbase-centroiding.Rmd’ using ‘UTF-8’... OK
  ‘v04-benchmarking.Rmd’ using ‘UTF-8’... OK
  ‘v05-MSnbase-development.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MSnbase.Rcheck/00check.log’
for details.



Installation output

MSnbase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MSnbase
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MSnbase’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -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 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -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;
      |                  ^~~
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++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/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 ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment”
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 ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment”
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)

Tests output

MSnbase.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> # 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

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, setdiff, sort, table,
    tapply, union, 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 2.28.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    trimws

> setMSnbaseVerbose(FALSE)
> ## register(SerialParam()) ## see issue 205
> 
> ## Erwinia
> f <- msdata::proteomics(full.names = TRUE,
+                         pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
> 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.name = 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: 0.26 Mb
- - - Spectra data - - -
 MS level(s): 1 2 
 Number of spectra: 509 
 MSn retention times: 18:28 - 22:03 minutes
- - - Processing information - - -
Data loaded [Thu Feb 22 00:24:55 2024] 
 MSnbase version: 2.28.1 
- - - Meta data  - - -
phenoData
  rowNames:
    TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz 
protocolData: none
featureData
  featureNames: F1.S001 F1.S002 ... F1.S509 (509 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
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: Thu Feb 22 00:29:00 2024 
 MSnbase version: 2.28.1 
- - - 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: Thu Feb 22 00:29:00 2024 
 MSnbase version: 2.28.1 
- - - 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 Thu Feb 22 00:29:22 2024 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Thu Feb 22 00:29:22 2024 
 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
reading dummyiTRAQ.mzid... DONE!
[ FAIL 0 | WARN 1092 | SKIP 12 | PASS 2388 ]

══ Skipped tests (12) ══════════════════════════════════════════════════════════
• empty test (12): 'test_MzTab.R:108:1', 'test_MzTab.R:123:1',
  'test_OnDiskMSnExp2.R:132:1', 'test_fdata-selection.R:71:1',
  '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:63:1', 'test_readMSData2.R:80:1'

[ FAIL 0 | WARN 1092 | SKIP 12 | PASS 2388 ]
Warning message:
In for (i in seq_len(n)) { :
  closing unused connection 4 (/tmp/RtmpcZxzVn/file5d30b70c04c96)
> 
> proc.time()
   user  system elapsed 
439.602  30.127 461.028 

Example timings

MSnbase.Rcheck/MSnbase-Ex.timings

nameusersystemelapsed
Chromatogram-class0.0750.0040.079
FeatComp-class0.1770.0040.181
FeaturesOfInterest-class0.0560.0000.056
MChromatograms-class0.1260.0000.126
MSmap-class000
MSnExp-class0.5440.0160.560
MSnProcess-class0.0010.0000.001
MSnSet-class8.8730.4329.304
MSnSetList-class1.4960.0561.552
MSpectra0.0830.0000.083
MzTab-class1.2770.0173.211
OnDiskMSnExp-class7.4840.2447.748
ProcessingStep-class0.0020.0000.002
ReporterIons-class0.0090.0000.009
TMT60.0050.0000.005
addIdentificationData-methods0.9200.0000.921
aggvar3.8630.1434.009
averageMSnSet4.5930.1014.698
bin-methods0.3450.0040.349
calculateFragments-methods1.2390.1881.427
chromatogram-MSnExp-method11.207 0.82012.028
clean-methods0.1180.0000.118
combineFeatures0.8910.0200.911
combineSpectra3.7630.2444.007
combineSpectraMovingWindow2.3450.1042.449
commonFeatureNames0.2170.0160.233
compareSpectra-methods0.1650.0000.165
consensusSpectrum0.0270.0000.026
estimateMzResolution4.2610.3004.548
estimateMzScattering1.3760.0521.428
estimateNoise-method0.0080.0000.008
extractPrecSpectra-methods1.0310.0761.107
extractSpectraData1.7980.1161.929
fData-utils0.3080.0000.308
factorsAsStrings0.0050.0040.010
featureCV0.0180.0000.018
fillUp0.0030.0000.003
formatRt0.0010.0000.000
get.amino.acids0.0020.0000.002
get.atomic.mass000
getVariableName0.0030.0000.003
hasSpectraOrChromatograms0.3270.0360.368
iPQF0.1990.0000.200
iTRAQ40.010.000.01
imageNA22.5710.0882.659
impute0.8480.0040.852
isCentroidedFromFile2.3890.1202.499
itraqdata0.0450.0000.045
listOf0.0010.0000.001
makeCamelCase0.0010.0000.000
makeNaData0.4290.0120.441
meanMzInts0.0370.0000.038
missing-data2.3950.0202.419
mzRident2dfr0.0240.0000.024
nFeatures0.5250.0080.533
nQuants0.0980.0000.097
naplot0.0660.0000.066
navMS2.5190.1242.690
normToReference0.1410.0070.149
normalise-methods0.0120.0000.011
npcv0.0040.0000.003
pSet-class0.0010.0000.001
pickPeaks-method0.2880.0040.291
plot-methods3.5440.1123.656
plot2d-methods0.4780.0000.478
plotDensity-methods0.6090.0080.617
plotMzDelta-methods0.7340.0000.734
plotNA-methods0.3450.0000.345
plotSpectrumSpectrum-methods1.3840.0441.427
precSelection0.0070.0000.006
purityCorrect-methods0.0150.0000.015
quantify-methods2.5960.0042.600
readMSData2.0340.0682.102
readMSnSet0.0640.0000.064
readMgfData1.4560.0201.476
readMzIdData0.5490.1480.699
readMzTabData1.0350.0531.341
readMzTabData_v0.90.2170.0100.348
readSRMData1.0140.1131.127
reduce-data.frame-method0.0140.0000.015
removeNoId-methods1.3710.3481.719
removePeaks-methods0.5340.0320.565
removeReporters-methods0.4440.0240.468
selectFeatureData1.2330.2551.488
smooth-methods0.2030.0040.207
trimMz-methods0.1500.0080.158
writeMgfData-methods1.5240.0281.551