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BioC 3.3: CHECK report for MSnbase on moscato2

This page was generated on 2016-10-13 12:49:46 -0700 (Thu, 13 Oct 2016).

Package 752/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 1.20.8
Laurent Gatto
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/MSnbase
Last Changed Rev: 119026 / Revision: 122332
Last Changed Date: 2016-06-29 13:33:21 -0700 (Wed, 29 Jun 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ ERROR ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 

Summary

Package: MSnbase
Version: 1.20.8
Command: rm -rf MSnbase.buildbin-libdir MSnbase.Rcheck && mkdir MSnbase.buildbin-libdir MSnbase.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.20.8.tar.gz >MSnbase.Rcheck\00install.out 2>&1 && cp MSnbase.Rcheck\00install.out MSnbase-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.20.8.tar.gz
StartedAt: 2016-10-13 06:37:00 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 06:49:46 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 766.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: MSnbase.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MSnbase.buildbin-libdir MSnbase.Rcheck && mkdir MSnbase.buildbin-libdir MSnbase.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.20.8.tar.gz >MSnbase.Rcheck\00install.out 2>&1 && cp MSnbase.Rcheck\00install.out MSnbase-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.20.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/MSnbase.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'MSnbase' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.7Mb
    libs   1.4Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/i386/MSnbase.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
readMzTabData    18.70   0.06   19.11
MzTab-class      11.14   0.04   13.15
MSnSet-class      8.33   0.02   11.28
averageMSnSet     7.67   0.08   16.85
quantify-methods  1.66   0.01    9.91
impute-methods    0.75   0.04    8.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
readMzTabData    15.52   0.17   15.70
MSnSet-class     10.90   0.05   10.95
averageMSnSet     8.75   0.21   12.73
MzTab-class       8.28   0.11    8.44
MSnSetList-class  5.51   0.01    5.53
quantify-methods  2.63   0.03   14.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-B/R/bin/i386/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  starting worker localhost:11794
  starting worker localhost:11794
  starting worker localhost:11794
  starting worker localhost:11794
  starting worker localhost:11794
  starting worker localhost:11794
  testthat results ================================================================
  OK: 623 SKIPPED: 0 FAILED: 2
  1. Failure: list2Spectrum2 function (@test_mzR-funs.R#11) 
  2. Error: makeNAdata2 (@test_nadata.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-B/R/bin/x64/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  starting worker localhost:11049
  starting worker localhost:11049
  starting worker localhost:11049
  starting worker localhost:11049
  starting worker localhost:11049
  starting worker localhost:11049
  starting worker localhost:11049
  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: 2 ERRORs, 3 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/MSnbase.Rcheck/00check.log'
for details.

testthat.Rout.fail:


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 06:47:58 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 06:47:58 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
starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
Object of class "FeaturesOfInterest"
 Created on Thu Oct 13 06:48:10 2016 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Thu Oct 13 06:48:10 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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%
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  |============================                                          |  40%
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  |==========================================                            |  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


starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
starting worker localhost:11049
testthat results ================================================================
OK: 623 SKIPPED: 0 FAILED: 1
1. Failure: list2Spectrum2 function (@test_mzR-funs.R#11) 

Error: testthat unit tests failed
Execution halted

testthat.Rout.fail:


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 0.18 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 06:46:15 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: 0.18 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 06:46:16 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
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
Object of class "FeaturesOfInterest"
 Created on Thu Oct 13 06:46:27 2016 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Thu Oct 13 06:46:27 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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  |                                                                            
  |==============                                                        |  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


2. Error: makeNAdata2 (@test_nadata.R#59) --------------------------------------
attempt to apply non-function
1: makeNaData2(dunkley2006[1:56], nRows = 1:10, nNA = 1:10, exclude = k) at testthat/test_nadata.R:59
2: combine(object, objectX)
3: combine(object, objectX)
4: combine(phenoData(x), phenoData(y))
5: combine(phenoData(x), phenoData(y))
6: .local(x, y, ...)
7: initialize(x, data = pData, varMetadata = vM)
8: initialize(x, data = pData, varMetadata = vM)
9: .local(.Object, ...)
10: callNextMethod(.Object, data = data, varMetadata = varMetadata, ...)
11: eval(call, callEnv)
12: eval(expr, envir, enclos)
13: .nextMethod(.Object, data = data, varMetadata = varMetadata, ...)
14: .local(.Object, ...)
15: callNextMethod(.Object, ...)
16: addNextMethod(method, f, envir = methodEnv)
17: addNextMethod(method, f, envir = methodEnv)
18: .findNextFromTable(method, f, optional, envir)
19: .findInheritedMethods(defined, fdef, mtable = NULL, excluded = excluded)
20: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
starting worker localhost:11794
testthat results ================================================================
OK: 623 SKIPPED: 0 FAILED: 2
1. Failure: list2Spectrum2 function (@test_mzR-funs.R#11) 
2. Error: makeNAdata2 (@test_nadata.R#59) 

Error: testthat unit tests failed
Execution halted

MSnbase.Rcheck/00install.out:


install for i386

* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o imp_neighbour_avg.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/i386
** 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

install for x64

* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o imp_neighbour_avg.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_1.20.8.zip
* DONE (MSnbase)

MSnbase.Rcheck/examples_i386/MSnbase-Ex.timings:

nameusersystemelapsed
FeatComp-class0.220.011.17
FeaturesOfInterest-class0.080.000.07
MSmap-class0.010.000.02
MSnExp-class0.340.020.59
MSnProcess-class000
MSnSet-class 8.33 0.0211.28
MSnSetList-class3.970.003.96
MzTab-class11.14 0.0413.15
NAnnotatedDataFrame-class0.030.000.04
ReporterIons-class0.030.000.03
TMT60.010.000.01
addIdentificationData-methods0.600.000.59
averageMSnSet 7.67 0.0816.85
bin-methods0.690.000.69
calculateFragments-methods0.540.020.56
chromatogram-methods0.160.030.84
clean-methods1.400.011.91
combineFeatures0.950.000.95
commonFeatureNames0.530.000.53
compareSpectra-methods0.200.000.21
estimateNoise-method0.020.000.01
exprsToRatios-methods0.090.000.10
extractPrecSpectra-methods0.460.000.45
featureCV0.040.000.05
fillUp000
formatRt0.020.000.01
get.amino.acids000
get.atomic.mass000
getVariableName000
iPQF0.290.000.30
iTRAQ40.020.000.01
imageNA22.450.032.87
impute-methods0.750.048.43
itraqdata0.110.000.11
listOf000
makeNaData1.440.031.47
missing-data2.230.012.31
nQuants0.220.000.22
naplot0.110.020.12
normalise-methods0.030.000.05
npcv000
pSet-class000
pickPeaks-method0.280.030.31
plot-methods1.530.001.53
plot2d-methods0.670.000.67
plotDensity-methods0.720.000.72
plotMzDelta-methods2.160.032.20
plotNA-methods0.570.020.57
plotSpectrumSpectrum-methods0.900.000.91
precSelection0.020.000.01
purityCorrect-methods0.040.000.05
quantify-methods1.660.019.91
readMSData0.450.000.45
readMSnSet0.560.002.68
readMgfData3.670.024.39
readMzTabData18.70 0.0619.11
readMzTabData_v0.90.240.000.32
removeNoId-methods1.060.021.08
removePeaks-methods1.340.011.58
removeReporters-methods0.810.000.81
selectFeatureData0.220.003.35
smooth-methods0.360.000.36
trimMz-methods0.250.020.27
writeMgfData-methods000
xic-methods000

MSnbase.Rcheck/examples_x64/MSnbase-Ex.timings:

nameusersystemelapsed
FeatComp-class0.340.000.34
FeaturesOfInterest-class0.130.010.14
MSmap-class000
MSnExp-class0.530.002.48
MSnProcess-class000
MSnSet-class10.90 0.0510.95
MSnSetList-class5.510.015.53
MzTab-class8.280.118.44
NAnnotatedDataFrame-class0.020.000.02
ReporterIons-class0.030.000.03
TMT60.010.000.01
addIdentificationData-methods0.850.000.85
averageMSnSet 8.75 0.2112.73
bin-methods1.110.001.11
calculateFragments-methods0.810.000.81
chromatogram-methods0.170.040.21
clean-methods1.750.021.77
combineFeatures1.140.001.14
commonFeatureNames0.750.011.17
compareSpectra-methods0.260.000.26
estimateNoise-method0.010.000.03
exprsToRatios-methods0.110.020.12
extractPrecSpectra-methods0.620.000.63
featureCV0.070.000.06
fillUp000
formatRt000
get.amino.acids000
get.atomic.mass000
getVariableName000
iPQF0.690.010.70
iTRAQ40.010.000.01
imageNA23.320.003.32
impute-methods0.980.041.21
itraqdata0.040.010.06
listOf000
makeNaData2.360.022.37
missing-data2.600.043.09
nQuants0.250.000.25
naplot0.160.000.15
normalise-methods0.030.000.03
npcv0.010.000.02
pSet-class000
pickPeaks-method0.380.000.37
plot-methods2.030.002.08
plot2d-methods1.680.001.68
plotDensity-methods1.690.001.84
plotMzDelta-methods1.440.041.47
plotNA-methods0.890.000.89
plotSpectrumSpectrum-methods1.290.001.29
precSelection0.020.000.02
purityCorrect-methods0.030.010.04
quantify-methods 2.63 0.0314.53
readMSData0.630.000.62
readMSnSet0.370.000.37
readMgfData3.170.053.60
readMzTabData15.52 0.1715.70
readMzTabData_v0.90.200.000.22
removeNoId-methods1.350.001.34
removePeaks-methods1.680.001.68
removeReporters-methods1.140.001.14
selectFeatureData0.220.000.22
smooth-methods0.510.000.51
trimMz-methods0.380.020.39
writeMgfData-methods000
xic-methods0.010.000.02