BioC 3.3: CHECK report for MSnbase on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.20.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.20.8’
* 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  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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’ ‘MALDIquant:::.which.closest’
  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
averageMSnSet 5.205  0.107   5.447
* 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:
    |======================================================================| 100%
  1. Failure: list2Spectrum2 function (@test_mzR-funs.R#11) ----------------------
  tic(sp) not equal to tic(sp2).
  1/1 mismatches
  [1] 26413754 - 0 == 26413754
  
  
  testthat results ================================================================
  OK: 623 SKIPPED: 0 FAILED: 1
  1. Failure: list2Spectrum2 function (@test_mzR-funs.R#11) 
  
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck/00check.log’
for details.


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 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
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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 1.20.8 
  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

> 
> 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 
  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 "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.
Object of class "MSnExp"
 Object size in memory: 0.2 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of MS1 acquisitions: 1 
 Number of MSn scans: 5 
 Number of precursor ions: 5 
 4 unique MZs
 Precursor MZ's: 437.8 - 716.34 
 MSn M/Z range: 100 2016.66 
 MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Thu Oct 13 04:37:08 2016 
 MSnbase version: 1.20.8 
- - - Meta data  - - -
phenoData
  rowNames: 1
  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)'
Object of class "MSnExp"
 Object size in memory: 0.2 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of MS1 acquisitions: 1 
 Number of MSn scans: 5 
 Number of precursor ions: 5 
 4 unique MZs
 Precursor MZ's: 437.8 - 716.34 
 MSn M/Z range: 100 2016.66 
 MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Thu Oct 13 04:37:08 2016 
 MSnbase version: 1.20.8 
- - - Meta data  - - -
phenoData
  rowNames: 1
  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)'
    common unique1 unique2
all      2       2       2
    common unique1 unique2
all      0       4       4
A        0       1       0
B        0       1       0
C        0       1       0
D        0       1       0
F        0       0       2
G        0       0       2
    common unique1 unique2
all      2       2       2
C        0       1       0
D        0       1       0
E        0       1       0
F        0       1       2
G        0       0       2
Object of class "FeaturesOfInterest"
 Created on Thu Oct 13 04:37:11 2016 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Thu Oct 13 04:37:11 2016 
 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
Reading 5 MS2 spectra from file dummyiTRAQ.mzXML

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  |============================                                          |  40%
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  |==========================================                            |  60%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |======================================================================| 100%
Reading 5 MS2 spectra from file dummyiTRAQ2.mzXML

  |                                                                            
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  |==============                                                        |  20%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |======================================================================| 100%
Creating 'MSnExp' object

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%
1. Failure: list2Spectrum2 function (@test_mzR-funs.R#11) ----------------------
tic(sp) not equal to tic(sp2).
1/1 mismatches
[1] 26413754 - 0 == 26413754


testthat results ================================================================
OK: 623 SKIPPED: 0 FAILED: 1
1. Failure: list2Spectrum2 function (@test_mzR-funs.R#11) 

Error: testthat unit tests failed
Execution halted

* installing *source* package ‘MSnbase’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o imp_neighbour_avg.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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’
Creating a generic function for ‘t’ from package ‘base’ in package ‘MSnbase’
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
Creating a generic function for ‘split’ from package ‘base’ in package ‘MSnbase’
** 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’
Creating a generic function for ‘t’ from package ‘base’ in package ‘MSnbase’
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
Creating a generic function for ‘split’ from package ‘base’ in package ‘MSnbase’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
FeatComp-class	0.177	0.008	0.224
FeaturesOfInterest-class	0.075	0.000	0.075
MSmap-class	0.001	0.000	0.001
MSnExp-class	0.327	0.004	0.335
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	4.610	0.040	4.662
MSnSetList-class	3.464	0.004	3.470
MzTab-class	0.949	0.000	3.762
NAnnotatedDataFrame-class	0.014	0.000	0.014
ReporterIons-class	0.012	0.000	0.012
TMT6	0.008	0.000	0.008
addIdentificationData-methods	0.518	0.000	0.517
averageMSnSet	5.205	0.107	5.447
bin-methods	0.723	0.004	0.727
calculateFragments-methods	0.538	0.016	0.553
chromatogram-methods	0.043	0.008	0.091
clean-methods	1.141	0.012	1.153
combineFeatures	0.637	0.012	0.651
commonFeatureNames	0.477	0.000	0.478
compareSpectra-methods	0.144	0.008	0.152
estimateNoise-method	0.014	0.000	0.023
exprsToRatios-methods	0.059	0.000	0.059
extractPrecSpectra-methods	0.434	0.000	0.434
featureCV	0.031	0.000	0.032
fillUp	0.005	0.000	0.005
formatRt	0.001	0.000	0.000
get.amino.acids	0.000	0.004	0.004
get.atomic.mass	0	0	0
getVariableName	0.002	0.000	0.002
iPQF	0.262	0.000	0.262
iTRAQ4	0.015	0.000	0.014
imageNA2	1.852	0.020	1.871
impute-methods	0.634	0.016	0.800
itraqdata	0.044	0.000	0.044
listOf	0.002	0.000	0.002
makeNaData	1.030	0.000	1.029
missing-data	1.826	0.012	1.839
nQuants	0.147	0.000	0.146
naplot	0.089	0.000	0.088
normalise-methods	0.02	0.00	0.02
npcv	0.003	0.000	0.002
pSet-class	0.001	0.004	0.002
pickPeaks-method	0.241	0.004	0.248
plot-methods	1.118	0.000	1.117
plot2d-methods	1.021	0.004	1.024
plotDensity-methods	0.679	0.000	0.678
plotMzDelta-methods	1.327	0.016	1.343
plotNA-methods	0.458	0.004	0.461
plotSpectrumSpectrum-methods	0.663	0.004	0.667
precSelection	0.013	0.000	0.012
purityCorrect-methods	0.022	0.000	0.023
quantify-methods	1.388	0.084	4.553
readMSData	0.421	0.004	0.425
readMSnSet	0.309	0.000	0.317
readMgfData	2.564	0.008	2.581
readMzTabData	2.448	0.008	3.383
readMzTabData_v0.9	0.187	0.000	0.509
removeNoId-methods	0.972	0.000	0.972
removePeaks-methods	1.050	0.008	1.057
removeReporters-methods	0.609	0.004	0.613
selectFeatureData	0.109	0.000	0.136
smooth-methods	0.251	0.004	0.256
trimMz-methods	0.165	0.000	0.164
writeMgfData-methods	0.001	0.000	0.001
xic-methods	0.000	0.000	0.001

BioC 3.3: CHECK report for MSnbase on zin2

Summary

Command output