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This page was generated on 2021-11-29 15:06:02 -0500 (Mon, 29 Nov 2021).

CHECK results for MSnbase on machv2

To the developers/maintainers of the MSnbase package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1222/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.20.3  (landing page)
Laurent Gatto
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/MSnbase
git_branch: RELEASE_3_14
git_last_commit: 760b1bb
git_last_commit_date: 2021-11-24 12:36:33 -0500 (Wed, 24 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: MSnbase
Version: 2.20.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSnbase_2.20.3.tar.gz
StartedAt: 2021-11-28 18:47:49 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 19:05:37 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 1067.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MSnbase.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSnbase_2.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MSnbase.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘2.20.3’
* 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
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    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 <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]
* 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
':::' 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 12.930  0.213  13.153
MSnSet-class               11.441  0.399  11.851
OnDiskMSnExp-class          9.762  0.245  10.028
averageMSnSet               7.297  0.198   7.515
estimateMzResolution        7.007  0.331   7.326
aggvar                      7.225  0.062   7.293
combineSpectra              5.931  0.109   6.057
MzTab-class                 0.811  0.045   6.901
* 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:
    reason: 1 resources failed to download
  Backtrace:
      █
   1. ├─ah[["AH49008"]] test_MSmap.R:7:0
   2. └─ah[["AH49008"]]
   3.   └─AnnotationHub:::.local(x, i, j = j, ...)
   4.     └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   5.       └─base::tryCatch(...)
   6.         └─base:::tryCatchList(expr, classes, parentenv, handlers)
   7.           └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.             └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 1095 | SKIP 12 | PASS 2362 ]
  Error: Test failures
  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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MSnbase.Rcheck/00check.log’
for details.


Installation output

MSnbase.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘MSnbase’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -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++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.1/Resources/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”
** 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”
** 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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

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, 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 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 2.20.3 
  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)
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
> 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$")
> extdata_mzXML_in_mem_ms2 <- readMSData(f, verbose = FALSE, centroided. = FALSE)
> extdata_mzXML_on_disk <- readMSData(f, centroided. = FALSE, mode = "onDisk")
> extdata_mzXML_on_disk_ms2 <- readMSData(f, msLevel = 2, centroided. = FALSE, mode = "onDisk")
> 
> sf <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> sciex <- readMSData(sf, mode = "onDisk")
> 
> test_check("MSnbase")
Experiment data
  Experimenter name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Contact information: Laurent Gatto 
  Contact email: lg390@cam.ac.uk 
  Title: Example 'MSnExp' data set 
  URL:  
  PMIDs:  
  No abstract available.
Instrument : 
  Model: test (1) 
  Manufacturer:  
  Customisations:  
  Use 'msInfo(object)' for more MIAPE-MS information.
Experiment data
  Experimenter name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Contact information: Laurent Gatto 
  Contact email: lg390@cam.ac.uk 
  Title: Example 'MSnExp' data set 
  URL:  
  PMIDs:  
  No abstract available.
  notes:
   Note1:
First note
MIAPE-MS information:
 1. General features:
  Date stamp:  
  Contact: Laurent Gatto 
  Name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Instument model: test 
  Manufacturer:  
  Customisations:  
  Software:  
  Version:  
  Switching:  
  Param file:  
 2. Ion source
  Source:  
  Source details:  
 3. Post-source componentry
  Analyzer:  
  Analyzer details:  
  Collision gas:  
  Pressure:   bars
  Energy:  
  Detector type:  
  Sensitivity:  
Error in x$.self$finalize() : 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  
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 [Sun Nov 28 18:54:13 2021] 
 MSnbase version: 2.20.3 
- - - 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: Sun Nov 28 18:59:51 2021 
 MSnbase version: 2.20.3 
- - - 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: Sun Nov 28 18:59:52 2021 
 MSnbase version: 2.20.3 
- - - 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 Sun Nov 28 19:00:16 2021 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Sun Nov 28 19:00:16 2021 
 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!
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (12)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_MSmap.R:7:1): (code run outside of `test_that()`) ───────────────
Error: failed to load resource
  name: AH49008
  title: PXD000001: raw mass spectrometry data
  reason: 1 resources failed to download
Backtrace:
    █
 1. ├─ah[["AH49008"]] test_MSmap.R:7:0
 2. └─ah[["AH49008"]]
 3.   └─AnnotationHub:::.local(x, i, j = j, ...)
 4.     └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 5.       └─base::tryCatch(...)
 6.         └─base:::tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)

[ FAIL 1 | WARN 1095 | SKIP 12 | PASS 2362 ]
Error: Test failures
Execution halted

Example timings

MSnbase.Rcheck/MSnbase-Ex.timings

nameusersystemelapsed
Chromatogram-class0.1210.0090.130
FeatComp-class0.3500.0200.373
FeaturesOfInterest-class0.0720.0060.079
MChromatograms-class0.2450.0070.253
MSmap-class0.0010.0020.002
MSnExp-class0.5980.0060.606
MSnProcess-class0.0020.0010.003
MSnSet-class11.441 0.39911.851
MSnSetList-class3.2390.1503.390
MSpectra0.1690.0130.182
MzTab-class0.8110.0456.901
OnDiskMSnExp-class 9.762 0.24510.028
ProcessingStep-class0.0030.0000.004
ReporterIons-class0.0140.0010.015
TMT60.0090.0020.012
addIdentificationData-methods0.8880.0120.905
aggvar7.2250.0627.293
averageMSnSet7.2970.1987.515
bin-methods0.5770.0080.586
calculateFragments-methods1.1960.0371.235
chromatogram-MSnExp-method12.930 0.21313.153
clean-methods0.2060.0080.215
combineFeatures1.7020.0231.726
combineSpectra5.9310.1096.057
combineSpectraMovingWindow3.1090.0483.163
commonFeatureNames0.4570.0200.478
compareSpectra-methods0.2800.0050.285
consensusSpectrum0.0470.0040.050
estimateMzResolution7.0070.3317.326
estimateMzScattering1.4850.0281.515
estimateNoise-method0.0130.0010.014
extractPrecSpectra-methods1.0400.0091.050
extractSpectraData2.3630.1072.438
fData-utils0.5320.0090.541
factorsAsStrings0.0140.0050.020
featureCV0.0330.0030.036
fillUp0.0040.0010.006
formatRt0.0010.0000.001
get.amino.acids0.0030.0020.005
get.atomic.mass000
getVariableName0.0050.0000.005
hasSpectraOrChromatograms0.3910.0220.417
iPQF0.4650.0080.474
iTRAQ40.0150.0010.016
imageNA24.2170.1854.408
impute0.6750.0310.705
isCentroidedFromFile2.5610.1162.666
itraqdata0.0810.0090.090
listOf0.0010.0010.002
makeCamelCase0.0010.0010.001
makeNaData0.9650.0090.975
meanMzInts0.0570.0030.060
missing-data4.1030.1124.222
mzRident2dfr0.0520.0050.057
nFeatures0.7810.0100.791
nQuants0.2090.0040.213
naplot0.0820.0070.089
navMS2.4870.0562.563
normToReference0.3270.0040.332
normalise-methods0.0240.0030.028
npcv0.0070.0000.007
pSet-class0.0010.0010.002
pickPeaks-method0.5730.0070.602
plot-methods4.6440.1084.759
plot2d-methods0.7340.0080.744
plotDensity-methods0.9170.0080.929
plotMzDelta-methods1.3230.0421.368
plotNA-methods0.5760.0060.584
plotSpectrumSpectrum-methods1.6080.0411.654
precSelection0.0120.0030.014
purityCorrect-methods0.0260.0040.029
quantify-methods4.0370.0324.072
readMSData2.1990.0242.225
readMSnSet0.1120.0040.117
readMgfData2.4990.0432.544
readMzIdData1.2610.8942.220
readMzTabData1.3400.0412.287
readMzTabData_v0.90.2160.0060.973
readSRMData1.7210.0321.755
reduce-data.frame-method0.0250.0020.027
removeNoId-methods1.3390.0211.359
removePeaks-methods1.0270.0071.034
removeReporters-methods0.6500.0030.653
selectFeatureData1.3740.0371.412
smooth-methods0.2950.0020.297
trimMz-methods0.2520.0040.256
writeMgfData-methods2.6490.0452.695