BioC 3.4: CHECK report for MSnbase on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.99.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.99.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  6.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.5Mb
* 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
OnDiskMSnExp-class 7.824  0.104   8.070
averageMSnSet      4.932  0.028   5.034
* 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:
   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
  testthat results ================================================================
  OK: 1001 SKIPPED: 0 FAILED: 1
  1. Failure: Compare OnDiskMSnExp and MSnExp extractPrecSpectra (@test_OnDiskMSnExp_other_methods.R#120) 
  
  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
  ‘/home/biocbuild/bbs-3.4-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, 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 1.99.1 
  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)
> 
> 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(): 2016-08-15
loading from cache '/home/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
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" (on disk)
Object size in memory: 0.12 Mb
- - - Spectra data - - -
 MS level(s): 1 2 
 Number of spectra: 509 
 MSn retention times: 18:28 - 22:3 minutes
- - - Processing information - - -
Data loaded [Tue Sep 20 09:46:56 2016] 
 MSnbase version: 1.99.1 
- - - 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: X001.1 X002.1 ... X509.1 (509 total)
  fvarLabels: fileIdx spIdx ... spectrum (26 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
1. Failure: Compare OnDiskMSnExp and MSnExp extractPrecSpectra (@test_OnDiskMSnExp_other_methods.R#120) 
unname(precMzs[sort(exP)]) not identical to unname(precursorMz(extsp2)).
Lengths differ: 20 vs 21


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 1.11.8.
Use 'pRolocdata()' to list available data sets.
Object of class "MSnExp" (in memory)
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: Tue Sep 20 09:48:31 2016 
 MSnbase version: 1.99.1 
- - - 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)'
Object of class "MSnExp" (in memory)
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: Tue Sep 20 09:48:31 2016 
 MSnbase version: 1.99.1 
- - - 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 Tue Sep 20 09:48:58 2016 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Tue Sep 20 09:48:58 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
testthat results ================================================================
OK: 1001 SKIPPED: 0 FAILED: 1
1. Failure: Compare OnDiskMSnExp and MSnExp extractPrecSpectra (@test_OnDiskMSnExp_other_methods.R#120) 

Error: testthat unit tests failed
Execution halted

* installing *source* package ‘MSnbase’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Spectrum1_class.c -o Spectrum1_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Spectrum2_class.c -o Spectrum2_class.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘compar_double_dd_for_stable_asc_order’:
utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function ‘compar_double_dd_for_stable_desc_order’:
utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function ‘compar_double_asc_order’:
utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: In function ‘compar_double_desc_order’:
utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: At top level:
utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function]
 static int compar_double_asc_order(const void *p1, const void *p2)
            ^
utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function]
 static int compar_double_desc_order(const void *p1, const void *p2)
            ^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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’
Creating a generic function for ‘all.equal’ 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’
Creating a generic function for ‘all.equal’ 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	0.184	0.000	0.237
FeaturesOfInterest-class	0.040	0.004	0.046
MSmap-class	0.000	0.000	0.001
MSnExp-class	0.396	0.004	0.399
MSnProcess-class	0.000	0.000	0.001
MSnSet-class	4.668	0.040	4.814
MSnSetList-class	3.340	0.004	3.343
MzTab-class	1.020	0.024	2.407
NAnnotatedDataFrame-class	0.016	0.000	0.015
OnDiskMSnExp-class	7.824	0.104	8.070
ProcessingStep-class	0.008	0.000	0.006
ReporterIons-class	0.012	0.000	0.012
TMT6	0.008	0.000	0.009
addIdentificationData-methods	0.464	0.000	0.467
averageMSnSet	4.932	0.028	5.034
bin-methods	0.688	0.004	0.695
calculateFragments-methods	0.472	0.004	0.479
chromatogram-methods	0.052	0.016	0.112
clean-methods	0.812	0.004	0.816
combineFeatures	0.844	0.008	0.851
commonFeatureNames	0.464	0.000	0.463
compareSpectra-methods	0.192	0.000	0.190
estimateNoise-method	0.004	0.000	0.003
exprsToRatios-methods	0.060	0.004	0.063
extractPrecSpectra-methods	0.424	0.000	0.425
featureCV	0.032	0.000	0.034
fillUp	0.008	0.000	0.006
formatRt	0.000	0.000	0.001
get.amino.acids	0.004	0.000	0.004
get.atomic.mass	0	0	0
getVariableName	0.004	0.000	0.002
iPQF	0.320	0.000	0.321
iTRAQ4	0.012	0.000	0.012
imageNA2	2.776	0.024	2.800
impute-methods	0.444	0.008	0.462
itraqdata	0.060	0.000	0.061
listOf	0.004	0.000	0.003
makeNaData	0.960	0.000	0.959
missing-data	2.932	0.008	2.938
nQuants	0.172	0.000	0.173
naplot	0.076	0.000	0.077
normalise-methods	0.016	0.000	0.017
npcv	0.004	0.000	0.003
pSet-class	0.004	0.000	0.002
pickPeaks-method	0.248	0.000	0.252
plot-methods	1.080	0.004	1.087
plot2d-methods	0.580	0.000	0.583
plotDensity-methods	0.592	0.000	0.593
plotMzDelta-methods	1.360	0.008	1.374
plotNA-methods	0.432	0.000	0.435
plotSpectrumSpectrum-methods	0.608	0.000	0.610
precSelection	0.008	0.000	0.011
purityCorrect-methods	0.024	0.000	0.026
quantify-methods	1.736	0.096	4.559
readMSData	0.896	0.000	0.895
readMSnSet	0.284	0.000	0.289
readMgfData	2.592	0.008	2.601
readMzTabData	2.216	0.020	2.477
readMzTabData_v0.9	0.152	0.004	0.380
removeNoId-methods	0.964	0.000	0.965
removePeaks-methods	0.952	0.004	0.956
removeReporters-methods	0.548	0.004	0.549
selectFeatureData	0.096	0.004	0.105
smooth-methods	0.240	0.004	0.244
trimMz-methods	0.184	0.000	0.186
writeMgfData-methods	0.000	0.000	0.001
xic-methods	0	0	0

BioC 3.4: CHECK report for MSnbase on zin1

Summary

Command output