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BioC 3.5: CHECK report for MSnbase on veracruz2

This page was generated on 2017-08-16 13:29:13 -0400 (Wed, 16 Aug 2017).

Package 861/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.2.0
Laurent Gatto
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MSnbase
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: MSnbase
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_2.2.0.tar.gz
StartedAt: 2017-08-16 05:41:52 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 05:58:52 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 1020.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: MSnbase.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.2.0’
* 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  8.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    4.4Mb
* 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 <lg390@cam.ac.uk> [aut, cre]
  Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre]
  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
Unexported objects imported by ':::' calls:
  ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
  ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
  ‘MALDIquant:::.savitzkyGolay’
  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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
OnDiskMSnExp-class 12.528  0.381  13.344
MSnSet-class        7.970  0.103   8.370
averageMSnSet       7.449  0.155   7.895
aggvar              5.419  0.057   5.629
quantify-methods    2.522  0.280   7.786
* 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:
  Error in signalCondition(e) : 
    no function to return from, jumping to top level
  Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
  testthat results ================================================================
  OK: 1325 SKIPPED: 0 FAILED: 7
  1. Failure: Combine MSnSet features (L) (@test_MSnSet.R#128) 
  2. Error: makeNAdata (@test_nadata.R#8) 
  3. Error: makeNAdata (@test_nadata.R#8) 
  4. Error: makeNAdata (@test_nadata.R#8) 
  5. Error: makeNAdata (@test_nadata.R#8) 
  6. Error: makeNAdata (@test_nadata.R#8) 
  7. Error: makeNAdata (@test_nadata.R#8) 
  
  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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

testthat.Rout.fail:


R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 2.2.0 
  Read '?MSnbase' and references therein for information
  about the package and how 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
> 
> 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:  

Attaching package: 'AnnotationHub'

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

    cache

snapshotDate(): 2017-04-25
loading from cache '/Users/biocbuild//.AnnotationHub/55314'
1
Object of class "MSmap"
 Map [75, 401]
  [1]  Retention time: 30:1 - 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: 30:1 - 34:58 
1
1
1. Failure: Combine MSnSet features (L) (@test_MSnSet.R#128) -------------------
combineFeatures(ee, L, redundancy.handler = "unique", cv = FALSE) showed 0 warnings


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: 0.13 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 Aug 16 05:53:38 2017] 
 MSnbase version: 2.2.0 
- - - 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: X001.1 X002.1 ... X509.1 (509 total)
  fvarLabels: fileIdx spIdx ... spectrum (27 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Object of class "ReporterIons"
TMT10HCD: '10-plex TMT HCD' with 10 reporter ions
 - 126.1277 +/- 0.002 (#8DD3C7)
 - 127.1248 +/- 0.002 (#FFFFB3)
 - 127.1311 +/- 0.002 (#BEBADA)
 - 128.1281 +/- 0.002 (#FB8072)
 - 128.1344 +/- 0.002 (#80B1D3)
 - 129.1315 +/- 0.002 (#FDB462)
 - 129.1378 +/- 0.002 (#B3DE69)
 - 130.1348 +/- 0.002 (#FCCDE5)
 - 130.1411 +/- 0.002 (#D9D9D9)
 - 131.1382 +/- 0.002 (#BC80BD)
Object of class "Spectrum1"
 Retention time: 0:0 
 MSn level: 1 
 Total ion count: 684 
 Polarity: 1 

This is pRolocdata version 1.14.0.
Use 'pRolocdata()' to list available data sets.
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 Aug 16 05:56:17 2017 
 MSnbase version: 2.2.0 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: X1.1 X2.1 ... X5.1 (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: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Aug 16 05:56:17 2017 
 MSnbase version: 2.2.0 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: X1.1 X2.1 ... X5.1 (5 total)
  fvarLabels: spectrum
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
1
Object of class "FeaturesOfInterest"
 Created on Wed Aug 16 05:57:08 2017 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Wed Aug 16 05:57:08 2017 
 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.
Iterations of EM: 
1...2...3...4...5...6...7...8...9...10...11...
[1] 0.07947339
2. Error: makeNAdata (@test_nadata.R#8) ----------------------------------------
attempt to apply non-function
1: makeNaData(dunkley2006, nNA = 1, exclude = 1:688) at testthat/test_nadata.R:8
2: combine(object, objectX)
3: combine(object, objectX)
4: combine(assayData(x), assayData(y))
5: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("environment", "environment"), structure(function (x, y, ...) 
   {
       if (length(list(...)) > 0L) {
           combine(x, do.call(combine, list(y, ...)))
       }
       else {
           standardGeneric("combine")
       }
   }, generic = structure("combine", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = c("x", 
   "y"), default = `\001NULL\001`, skeleton = (function (x, y, ...) 
   stop("invalid call in method dispatch to 'combine' (no default method)", domain = NA))(x, 
       y, ...), class = structure("nonstandardGenericFunction", package = "methods")), 
       <environment>)
6: .findInheritedMethods(classes, fdef, mtable)
7: .duplicateClassesExist()
8: get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable)
9: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
3. Error: makeNAdata (@test_nadata.R#8) ----------------------------------------
attempt to apply non-function
1: makeNaData(dunkley2006, nNA = 1, exclude = 1:688) at testthat/test_nadata.R:8
2: combine(object, objectX)
3: combine(object, objectX)
4: combine(assayData(x), assayData(y))
5: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("environment", "environment"), structure(function (x, y, ...) 
   {
       if (length(list(...)) > 0L) {
           combine(x, do.call(combine, list(y, ...)))
       }
       else {
           standardGeneric("combine")
       }
   }, generic = structure("combine", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = c("x", 
   "y"), default = `\001NULL\001`, skeleton = (function (x, y, ...) 
   stop("invalid call in method dispatch to 'combine' (no default method)", domain = NA))(x, 
       y, ...), class = structure("nonstandardGenericFunction", package = "methods")), 
       <environment>)
6: .findInheritedMethods(classes, fdef, mtable)
7: .duplicateClassesExist()
8: get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable)
9: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
4. Error: makeNAdata (@test_nadata.R#8) ----------------------------------------
attempt to apply non-function
1: makeNaData(dunkley2006, nNA = 1, exclude = 1:688) at testthat/test_nadata.R:8
2: combine(object, objectX)
3: combine(object, objectX)
4: combine(assayData(x), assayData(y))
5: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("environment", "environment"), structure(function (x, y, ...) 
   {
       if (length(list(...)) > 0L) {
           combine(x, do.call(combine, list(y, ...)))
       }
       else {
           standardGeneric("combine")
       }
   }, generic = structure("combine", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = c("x", 
   "y"), default = `\001NULL\001`, skeleton = (function (x, y, ...) 
   stop("invalid call in method dispatch to 'combine' (no default method)", domain = NA))(x, 
       y, ...), class = structure("nonstandardGenericFunction", package = "methods")), 
       <environment>)
6: .findInheritedMethods(classes, fdef, mtable)
7: .duplicateClassesExist()
8: get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable)
9: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
5. Error: makeNAdata (@test_nadata.R#8) ----------------------------------------
attempt to apply non-function
1: makeNaData(dunkley2006, nNA = 1, exclude = 1:688) at testthat/test_nadata.R:8
2: combine(object, objectX)
3: combine(object, objectX)
4: combine(assayData(x), assayData(y))
5: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("environment", "environment"), structure(function (x, y, ...) 
   {
       if (length(list(...)) > 0L) {
           combine(x, do.call(combine, list(y, ...)))
       }
       else {
           standardGeneric("combine")
       }
   }, generic = structure("combine", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = c("x", 
   "y"), default = `\001NULL\001`, skeleton = (function (x, y, ...) 
   stop("invalid call in method dispatch to 'combine' (no default method)", domain = NA))(x, 
       y, ...), class = structure("nonstandardGenericFunction", package = "methods")), 
       <environment>)
6: .findInheritedMethods(classes, fdef, mtable)
7: .duplicateClassesExist()
8: get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable)
9: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
6. Error: makeNAdata (@test_nadata.R#8) ----------------------------------------
attempt to apply non-function
1: makeNaData(dunkley2006, nNA = 1, exclude = 1:688) at testthat/test_nadata.R:8
2: combine(object, objectX)
3: combine(object, objectX)
4: combine(assayData(x), assayData(y))
5: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("environment", "environment"), structure(function (x, y, ...) 
   {
       if (length(list(...)) > 0L) {
           combine(x, do.call(combine, list(y, ...)))
       }
       else {
           standardGeneric("combine")
       }
   }, generic = structure("combine", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = c("x", 
   "y"), default = `\001NULL\001`, skeleton = (function (x, y, ...) 
   stop("invalid call in method dispatch to 'combine' (no default method)", domain = NA))(x, 
       y, ...), class = structure("nonstandardGenericFunction", package = "methods")), 
       <environment>)
6: .findInheritedMethods(classes, fdef, mtable)
7: .duplicateClassesExist()
8: get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable)
9: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
7. Error: makeNAdata (@test_nadata.R#8) ----------------------------------------
attempt to apply non-function
1: makeNaData(dunkley2006, nNA = 1, exclude = 1:688) at testthat/test_nadata.R:8
2: combine(object, objectX)
3: combine(object, objectX)
4: combine(assayData(x), assayData(y))
5: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("environment", "environment"), structure(function (x, y, ...) 
   {
       if (length(list(...)) > 0L) {
           combine(x, do.call(combine, list(y, ...)))
       }
       else {
           standardGeneric("combine")
       }
   }, generic = structure("combine", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = c("x", 
   "y"), default = `\001NULL\001`, skeleton = (function (x, y, ...) 
   stop("invalid call in method dispatch to 'combine' (no default method)", domain = NA))(x, 
       y, ...), class = structure("nonstandardGenericFunction", package = "methods")), 
       <environment>)
6: .findInheritedMethods(classes, fdef, mtable)
7: .duplicateClassesExist()
8: get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable)
9: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
testthat results ================================================================
OK: 1325 SKIPPED: 0 FAILED: 7
1. Failure: Combine MSnSet features (L) (@test_MSnSet.R#128) 
2. Error: makeNAdata (@test_nadata.R#8) 
3. Error: makeNAdata (@test_nadata.R#8) 
4. Error: makeNAdata (@test_nadata.R#8) 
5. Error: makeNAdata (@test_nadata.R#8) 
6. Error: makeNAdata (@test_nadata.R#8) 
7. Error: makeNAdata (@test_nadata.R#8) 

Error: testthat unit tests failed
Execution halted

MSnbase.Rcheck/00install.out:

* installing *source* package ‘MSnbase’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -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/3.4/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 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/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++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -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/3.4/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++ -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 /Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck/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 ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing 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 ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)

MSnbase.Rcheck/MSnbase-Ex.timings:

nameusersystemelapsed
FeatComp-class0.2910.0240.319
FeaturesOfInterest-class0.0830.0060.092
MSmap-class0.0010.0000.002
MSnExp-class0.3790.0040.395
MSnProcess-class0.0020.0000.002
MSnSet-class7.9700.1038.370
MSnSetList-class4.1760.0254.316
MzTab-class1.2100.0294.087
NAnnotatedDataFrame-class0.0240.0010.024
OnDiskMSnExp-class12.528 0.38113.344
ProcessingStep-class0.0070.0000.007
ReporterIons-class0.0160.0000.016
TMT60.0190.0000.022
addIdentificationData-methods0.7790.0040.808
aggvar5.4190.0575.629
averageMSnSet7.4490.1557.895
bin-methods0.9350.0150.975
calculateFragments-methods0.7950.0140.829
chromatogram-methods0.1070.0170.127
clean-methods0.9050.0370.971
combineFeatures0.9960.0111.027
commonFeatureNames0.4710.0160.497
compareSpectra-methods0.2590.0080.270
estimateNoise-method0.0110.0000.012
exprsToRatios-methods0.1070.0020.116
extractPrecSpectra-methods0.5970.0030.615
featureCV0.0310.0010.032
fillUp0.0150.0010.015
formatRt0.0010.0000.001
get.amino.acids0.0050.0010.005
get.atomic.mass0.0010.0000.000
getVariableName0.0040.0000.005
iPQF0.5180.0050.537
iTRAQ40.0120.0000.012
imageNA23.5200.0663.721
impute-methods0.8210.0140.906
itraqdata0.1190.0030.126
listOf0.0030.0000.003
makeNaData1.2230.0061.273
missing-data3.5220.0363.665
nFeatures0.5310.0290.575
nQuants0.1410.0010.147
naplot0.0770.0030.083
navMS3.4360.0743.613
normalise-methods0.0200.0010.021
npcv0.0070.0000.007
pSet-class0.0020.0000.003
pickPeaks-method0.2860.0060.298
plot-methods1.6390.0051.689
plot2d-methods0.8060.0040.834
plotDensity-methods1.1540.0031.192
plotMzDelta-methods1.2720.0421.360
plotNA-methods0.5920.0030.610
plotSpectrumSpectrum-methods0.8880.0060.916
precSelection0.0240.0010.032
purityCorrect-methods0.1110.0030.117
quantify-methods2.5220.2807.786
readMSData1.0340.0041.065
readMSnSet0.3630.0060.377
readMgfData3.1710.0283.313
readMzTabData2.6040.0353.202
readMzTabData_v0.90.3420.0040.703
removeNoId-methods1.1870.0041.216
removePeaks-methods0.7860.0110.812
removeReporters-methods0.7900.0050.815
selectFeatureData0.1130.0050.121
smooth-methods0.2410.0060.267
trimMz-methods0.1960.0030.201
writeMgfData-methods0.0010.0000.001
xic-methods0.0010.0000.001