BioC 3.3: CHECK report for MSnbase on oaxaca

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.20.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ... OK
* 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    7.204  0.137   9.185
MSnSet-class     6.287  0.103   6.639
quantify-methods 1.796  0.198   5.888
MzTab-class      1.308  0.026   6.095
* 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, 1 NOTE
See
  ‘/Users/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-apple-darwin13.4.0 (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, 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 04:02:26 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 04:02:27 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 04:02:30 2016 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Thu Oct 13 04:02:30 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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |======================================================================| 100%
Reading 5 MS2 spectra from file dummyiTRAQ2.mzXML

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
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 imp_neighbour_avg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.249	0.015	0.428
FeaturesOfInterest-class	0.061	0.003	0.065
MSmap-class	0.001	0.000	0.002
MSnExp-class	0.356	0.005	0.421
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	6.287	0.103	6.639
MSnSetList-class	4.729	0.027	4.761
MzTab-class	1.308	0.026	6.095
NAnnotatedDataFrame-class	0.022	0.001	0.022
ReporterIons-class	0.021	0.001	0.022
TMT6	0.013	0.000	0.014
addIdentificationData-methods	0.629	0.010	0.640
averageMSnSet	7.204	0.137	9.185
bin-methods	0.751	0.011	0.761
calculateFragments-methods	0.637	0.013	0.650
chromatogram-methods	0.081	0.015	0.210
clean-methods	0.992	0.036	1.028
combineFeatures	0.957	0.012	0.970
commonFeatureNames	0.713	0.013	0.727
compareSpectra-methods	0.194	0.006	0.200
estimateNoise-method	0.022	0.001	0.023
exprsToRatios-methods	0.093	0.002	0.095
extractPrecSpectra-methods	0.528	0.004	0.532
featureCV	0.046	0.001	0.048
fillUp	0.009	0.001	0.009
formatRt	0.001	0.000	0.002
get.amino.acids	0.006	0.001	0.006
get.atomic.mass	0.000	0.000	0.001
getVariableName	0.002	0.000	0.002
iPQF	0.427	0.004	0.431
iTRAQ4	0.019	0.000	0.019
imageNA2	2.349	0.067	2.474
impute-methods	0.759	0.019	1.126
itraqdata	0.050	0.004	0.054
listOf	0.011	0.000	0.011
makeNaData	1.562	0.007	1.571
missing-data	2.072	0.050	3.037
nQuants	0.191	0.001	0.266
naplot	0.099	0.005	0.105
normalise-methods	0.027	0.001	0.029
npcv	0.003	0.000	0.003
pSet-class	0.003	0.000	0.003
pickPeaks-method	0.321	0.002	0.338
plot-methods	1.770	0.010	1.784
plot2d-methods	0.825	0.003	0.829
plotDensity-methods	0.839	0.004	0.844
plotMzDelta-methods	1.149	0.038	1.189
plotNA-methods	0.525	0.004	0.529
plotSpectrumSpectrum-methods	0.836	0.009	0.866
precSelection	0.017	0.001	0.018
purityCorrect-methods	0.032	0.002	0.034
quantify-methods	1.796	0.198	5.888
readMSData	0.476	0.003	0.479
readMSnSet	0.465	0.007	0.557
readMgfData	3.578	0.040	3.623
readMzTabData	3.246	0.030	3.994
readMzTabData_v0.9	0.260	0.003	0.640
removeNoId-methods	1.068	0.007	1.075
removePeaks-methods	1.226	0.014	1.241
removeReporters-methods	1.285	0.009	1.300
selectFeatureData	0.142	0.016	0.178
smooth-methods	0.298	0.007	0.305
trimMz-methods	0.208	0.002	0.210
writeMgfData-methods	0.002	0.000	0.001
xic-methods	0.001	0.000	0.001

BioC 3.3: CHECK report for MSnbase on oaxaca

Summary

Command output