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CHECK report for MSnbase on celaya2

This page was generated on 2019-10-16 12:48:44 -0400 (Wed, 16 Oct 2019).

Package 1055/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.10.1
Laurent Gatto
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MSnbase
Branch: RELEASE_3_9
Last Commit: 4d5899b
Last Changed Date: 2019-05-31 07:14:27 -0400 (Fri, 31 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: MSnbase
Version: 2.10.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSnbase_2.10.1.tar.gz
StartedAt: 2019-10-16 04:53:23 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:15:55 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 1351.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: MSnbase.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSnbase_2.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘2.10.1’
* 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
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.9Mb
* 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  [aut, cre] ()
  Johannes Rainer  [aut, cre] ()
  Sebastian Gibb  [aut, cre]
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
  ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
  ‘MALDIquant:::.savitzkyGolay’
  ‘S4Vectors:::makeClassinfoRowForCompactPrinting’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  ‘mzR:::.hasChromatograms’ ‘mzR:::.hasSpectra’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.data.frame.MSnExp as.data.frame.MSnSet as.data.frame.Spectrum
  as.data.frame.mzRident as.matrix.FoICollection droplevels.MSnSet
  is.na.MSnSet t.MSnSet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 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 or elapsed time > 5s
                             user system elapsed
estimateMzScattering       25.245  1.792  27.266
chromatogram-MSnExp-method 20.747  4.071  23.966
MSnSet-class               13.558  0.720  14.648
OnDiskMSnExp-class         11.731  0.420  12.224
quantify-methods            7.427  3.369   5.768
averageMSnSet               9.538  0.371  10.163
aggvar                      9.700  0.159  10.165
estimateMzResolution        8.297  1.447   9.678
MSnSetList-class            5.766  0.111   5.879
plot-methods                5.266  0.296   5.569
missing-data                4.776  0.365   5.142
imageNA2                    4.682  0.402   5.145
* 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         2        NA          3 |         1
    2         2   1.23245          4 |         2
    3         1   1.23245          5 |         3
  reading dummyiTRAQ.mzid... DONE!
  Iterations of EM: 
  1...2...3...4...5...6...7...8...9...10...11...
  [1] 0.07947339
  ...Error in x$.self$finalize() : attempt to apply non-function
  Error in x$.self$finalize() : attempt to apply non-function
  ...══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2196 | SKIPPED: 9 | WARNINGS: 1058 | FAILED: 1 ]
  1. Error: (unknown) (@test_MSmap.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.Rcheck/00check.log’
for details.


Installation output

MSnbase.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSnbase
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MSnbase’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: unused function '_new_Spectrum1' [-Wunused-function]
static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: unused function '_new_Spectrum2' [-Wunused-function]
static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c utils.c -o utils.o
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:121:12: warning: unused function 'compar_double_asc_order' [-Wunused-function]
static int compar_double_asc_order(const void *p1, const void *p2)
           ^
utils.c:131:12: warning: unused function 'compar_double_desc_order' [-Wunused-function]
static int compar_double_desc_order(const void *p1, const void *p2)
           ^
6 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-MSnbase/00new/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
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”
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
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”
** 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.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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, 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:base':

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.10.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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: [email protected] 
  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: [email protected] 
  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:  
── 1. Error: (unknown) (@test_MSmap.R#7)  ──────────────────────────────────────
failed to load resource
  name: AH49008
  title: PXD000001: raw mass spectrometry data
  reason: Recv failure: Connection reset by peer
1: ah[["AH49008"]] at testthat/test_MSmap.R:7
2: ah[["AH49008"]]
3: .local(x, i, j, ...)
4: .Hub_get1(x[idx], force = force, verbose = verbose)
5: tryCatch({
       fls <- cache(getHub(class), force = force, verbose = verbose)
       .get1(class)
   }, error = function(err) {
       stop("failed to load resource", "\n  name: ", names(x), "\n  title: ", x$title, 
           "\n  reason: ", conditionMessage(err), call. = FALSE)
   })
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
9: stop("failed to load resource", "\n  name: ", names(x), "\n  title: ", x$title, "\n  reason: ", 
       conditionMessage(err), call. = FALSE)

Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
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  
Instance of class 'MSnSetList' containig 3 objects.
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.25 Mb
- - - Spectra data - - -
 MS level(s): 1 2 
 Number of spectra: 509 
 MSn retention times: 18:28 - 22:3 minutes
- - - Processing information - - -
Data loaded [Wed Oct 16 05:01:10 2019] 
 MSnbase version: 2.10.1 
- - - 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 (33 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
......Error in x$.self$finalize() : attempt to apply non-function
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: 0:0 
 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: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 16 05:08:36 2019 
 MSnbase version: 2.10.1 
- - - 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: 0.21 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 5 
 MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 16 05:08:37 2019 
 MSnbase version: 2.10.1 
- - - 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 Wed Oct 16 05:09:11 2019 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Wed Oct 16 05:09:11 2019 
 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.
Spectra 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
Spectra 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
Spectra 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
reading dummyiTRAQ.mzid... DONE!
Iterations of EM: 
1...2...3...4...5...6...7...8...9...10...11...
[1] 0.07947339
...Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
...══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2196 | SKIPPED: 9 | WARNINGS: 1058 | FAILED: 1 ]
1. Error: (unknown) (@test_MSmap.R#7) 

Error: testthat unit tests failed
Execution halted

Example timings

MSnbase.Rcheck/MSnbase-Ex.timings

nameusersystemelapsed
Chromatogram-class0.0650.0050.069
Chromatograms-class0.2950.0070.302
FeatComp-class0.3970.0420.447
FeaturesOfInterest-class0.0950.0150.109
MSmap-class0.0010.0000.002
MSnExp-class0.7060.0140.723
MSnProcess-class0.0020.0000.002
MSnSet-class13.558 0.72014.648
MSnSetList-class5.7660.1115.879
MzTab-class0.5690.0552.981
OnDiskMSnExp-class11.731 0.42012.224
ProcessingStep-class0.0070.0000.007
ReporterIons-class0.0120.0000.013
Spectra0.1130.0090.122
TMT60.0130.0030.015
addIdentificationData-methods1.0600.0091.073
aggvar 9.700 0.15910.165
averageMSnSet 9.538 0.37110.163
bin-methods0.6700.0830.765
calculateFragments-methods1.8980.0462.068
chromatogram-MSnExp-method20.747 4.07123.966
clean-methods0.3600.1030.463
combineFeatures2.7690.4943.272
combineSpectra0.3140.0460.360
combineSpectraMovingWindow3.8510.5494.415
commonFeatureNames0.4810.0210.503
compareSpectra-methods0.2920.0200.313
consensusSpectrum0.0600.0020.064
estimateMzResolution8.2971.4479.678
estimateMzScattering25.245 1.79227.266
estimateNoise-method0.0200.0010.020
exprsToRatios-methods0.0820.0050.087
extractPrecSpectra-methods1.5360.1611.697
fData-utils0.5740.0190.611
factorsAsStrings0.0230.0030.026
featureCV0.0390.0030.042
fillUp0.0090.0020.011
formatRt0.0010.0010.002
get.amino.acids0.0070.0030.009
get.atomic.mass0.0010.0010.001
getVariableName0.0060.0000.006
hasSpectraOrChromatograms0.4910.0300.528
iPQF0.4390.0050.444
iTRAQ40.0190.0010.019
imageNA24.6820.4025.145
impute-methods0.9410.0370.997
isCentroidedFromFile3.8760.4014.217
itraqdata0.0750.0250.101
listOf0.0030.0000.003
makeCamelCase0.0010.0000.002
makeNaData1.6150.0341.649
meanMzInts0.0700.0060.077
missing-data4.7760.3655.142
mzRident2dfr0.0400.0020.041
nFeatures0.7460.0740.820
nQuants0.2350.0050.239
naplot0.0950.0090.103
navMS3.0360.2483.373
normToReference0.3250.0050.330
normalise-methods0.0270.0030.030
npcv0.0080.0000.008
pSet-class0.0020.0010.004
pickPeaks-method0.4300.0190.450
plot-methods5.2660.2965.569
plot2d-methods1.0040.0241.029
plotDensity-methods1.0270.0371.064
plotMzDelta-methods1.5840.1361.720
plotNA-methods0.8680.0060.875
plotSpectrumSpectrum-methods1.6920.0131.711
precSelection0.0150.0040.019
purityCorrect-methods0.0380.0070.047
quantify-methods7.4273.3695.768
readMSData2.1940.0142.208
readMSnSet0.1250.0060.135
readMgfData2.8540.1953.051
readMzIdData2.8251.1263.958
readMzTabData1.4720.1652.399
readMzTabData_v0.90.4480.0200.827
readSRMData1.9480.0491.998
reduce-data.frame-method0.0320.0010.033
removeNoId-methods1.6360.0901.727
removePeaks-methods1.1180.0501.171
removeReporters-methods1.3200.0591.380
selectFeatureData1.4890.0711.562
smooth-methods0.3870.0270.414
trimMz-methods0.1860.0180.204
writeMgfData-methods0.0010.0000.001