Multiple platform build/check report for BioC 3.7 - CHECK report for MSnbase on tokay2

Package: MSnbase

Version: 2.6.4

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MSnbase_2.6.4.tar.gz

StartedAt: 2018-10-17 03:31:51 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:04:51 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 1980.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: MSnbase.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MSnbase_2.6.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/MSnbase.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.6.4'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/MSnExp-class.Rd:243: file link 'isolationWindow' in package 'mzR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/MSnSet-class.Rd:510: file link 'write.exprs' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/OnDiskMSnExp-class.Rd:489: file link 'normalize' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/chromatogram-MSnExp-method.Rd:70: file link 'Chromatogram' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/combineFeatures.Rd:49: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/combineFeatures.Rd:156: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/estimateNoise-method.Rd:45: file link 'estimateNoise' in package 'MALDIquant' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/MSnbase.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   1.9Mb
    libs   1.5Mb
* 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
* 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'
  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 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
estimateMzScattering       19.63   0.12   22.13
MSnSet-class                9.18   0.17    9.38
OnDiskMSnExp-class          8.38   0.49   16.43
estimateMzResolution        7.84   0.69   10.56
chromatogram-MSnExp-method  7.99   0.48   31.62
readMzTabData               6.66   0.03    6.86
averageMSnSet               4.69   0.41    7.18
MzTab-class                 4.46   0.11    5.95
plot-methods                4.30   0.03    8.83
combineSpectraMovingWindow  2.75   0.09   36.71
navMS                       2.65   0.14   34.39
quantify-methods            1.57   0.03    9.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
estimateMzScattering       16.96   0.10   17.06
chromatogram-MSnExp-method 11.55   0.58   35.67
MSnSet-class                9.55   0.19   13.20
OnDiskMSnExp-class          8.51   0.35    8.86
estimateMzResolution        6.41   0.28    6.65
readMzTabData               5.58   0.05    5.75
averageMSnSet               5.25   0.23   10.36
quantify-methods            2.36   0.02   10.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/MSnbase.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/MSnbase_2.6.4.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.6.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL MSnbase_2.6.4.zip && rm MSnbase_2.6.4.tar.gz MSnbase_2.6.4.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1750k  100 1750k    0     0  25.0M      0 --:--:-- --:--:-- --:--:-- 27.5M

install for i386

* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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)
            ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-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'
in method for 'coerce' with signature '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
** inst
** byte-compile and prepare 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 '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
** help
*** installing help indices
  converting help for package 'MSnbase'
    finding HTML links ... done
    Chromatogram-class                      html  
    Chromatograms-class                     html  
    FeatComp-class                          html  
    FeaturesOfInterest-class                html  
    finding level-2 HTML links ... done

    MIAPE-class                             html  
    MSmap-class                             html  
    MSnExp-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/MSnExp-class.Rd:243: file link 'isolationWindow' in package 'mzR' does not exist and so has been treated as a topic
    MSnProcess-class                        html  
    MSnSet-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/MSnSet-class.Rd:510: file link 'write.exprs' in package 'MSnbase' does not exist and so has been treated as a topic
    MSnSetList-class                        html  
    MSnbaseOptions                          html  
    MzTab-class                             html  
    NAnnotatedDataFrame-class               html  
    OnDiskMSnExp-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/OnDiskMSnExp-class.Rd:489: file link 'normalize' in package 'MSnbase' does not exist and so has been treated as a topic
    ProcessingStep-class                    html  
    ReporterIons-class                      html  
    Spectrum-class                          html  
    Spectrum1-class                         html  
    Spectrum2-class                         html  
    TMT6                                    html  
    addIdentificationData-methods           html  
    aggvar                                  html  
    averageMSnSet                           html  
    bin-methods                             html  
    calculateFragments-methods              html  
    chromatogram-MSnExp-method              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/chromatogram-MSnExp-method.Rd:70: file link 'Chromatogram' in package 'MSnbase' does not exist and so has been treated as a topic
    clean-methods                           html  
    combineFeatures                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/combineFeatures.Rd:49: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/combineFeatures.Rd:156: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
    combineSpectra                          html  
    combineSpectraMovingWindow              html  
    commonFeatureNames                      html  
    compareMSnSets                          html  
    compareSpectra-methods                  html  
    defunct                                 html  
    estimateMzResolution                    html  
    estimateMzScattering                    html  
    estimateNoise-method                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw3bIvf/R.INSTALL1e0c10ae31c4/MSnbase/man/estimateNoise-method.Rd:45: file link 'estimateNoise' in package 'MALDIquant' does not exist and so has been treated as a topic
    exprsToRatios-methods                   html  
    extractPrecSpectra-methods              html  
    factorsAsStrings                        html  
    featureCV                               html  
    fillUp                                  html  
    filterIdentificationDataFrame           html  
    formatRt                                html  
    get.amino.acids                         html  
    get.atomic.mass                         html  
    getVariableName                         html  
    grepEcols                               html  
    iPQF                                    html  
    iTRAQ4                                  html  
    imageNA2                                html  
    impute-methods                          html  
    isCentroidedFromFile                    html  
    itraqdata                               html  
    listOf                                  html  
    makeCamelCase                           html  
    makeNaData                              html  
    missing-data                            html  
    mzRident2dfr                            html  
    nFeatures                               html  
    nQuants                                 html  
    naplot                                  html  
    navMS                                   html  
    normToReference                         html  
    normalise-methods                       html  
    npcv                                    html  
    pSet-class                              html  
    pickPeaks-method                        html  
    plot-methods                            html  
    plot2d-methods                          html  
    plotDensity-methods                     html  
    plotMzDelta-methods                     html  
    plotNA-methods                          html  
    plotSpectrumSpectrum-methods            html  
    precSelection                           html  
    purityCorrect-methods                   html  
    quantify-methods                        html  
    readMSData                              html  
    readMSnSet                              html  
    readMgfData                             html  
    readMzIdData                            html  
    readMzTabData                           html  
    readMzTabData_v0.9                      html  
    readSRMData                             html  
    reduce-data.frame-method                html  
    removeNoId-methods                      html  
    removePeaks-methods                     html  
    removeReporters-methods                 html  
    selectFeatureData                       html  
    smooth-methods                          html  
    trimMz-methods                          html  
    updateObject-methods                    html  
    writeMSData                             html  
    writeMgfData-methods                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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)
            ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_2.6.4.zip
* DONE (MSnbase)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'MSnbase' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 2.6.4 
  Visit https://lgatto.github.io/MSnbase/ 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
> 
> ## Erwinia
> f <- msdata::proteomics(full.names = TRUE,
+                         pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
> tmt_erwinia_in_mem_ms1 <- readMSData(f, msLevel = 1)
> tmt_erwinia_in_mem_ms2 <- readMSData(f, msLevel = 2)
> tmt_erwinia_on_disk <- readMSData(f, mode = "onDisk")
> tmt_erwinia_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk")
> tmt_erwinia_on_disk_ms2 <- readMSData(f, msLevel = 2, mode = "onDisk")
> ## subset by rt
> tmt_im_ms1_sub <- filterRt(tmt_erwinia_in_mem_ms1, c(1200, 1250))
> tmt_im_ms2_sub <- filterRt(tmt_erwinia_in_mem_ms2, c(1200, 1250))
> tmt_od_sub <- filterRt(tmt_erwinia_on_disk, c(1200, 1250))
> tmt_od_ms1_sub <- filterRt(tmt_erwinia_on_disk_ms1, c(1200, 1250))
> tmt_od_ms2_sub <- filterRt(tmt_erwinia_on_disk_ms2, c(1200, 1250))
> 
> ## microtofq
> f <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+        system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_in_mem_ms1 <- readMSData(f, msLevel = 1)
> microtofq_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk")
> microtofq_on_disk <- readMSData(f, mode = "onDisk")
> 
> ## extdata mzML
> f <- dir(system.file(package = "MSnbase", dir = "extdata"),
+          full.name = TRUE, pattern = "mzXML$")
> extdata_mzXML_in_mem_ms2 <- readMSData(f, verbose = FALSE, centroided. = FALSE)
> extdata_mzXML_on_disk <- readMSData(f, centroided. = FALSE, mode = "onDisk")
> extdata_mzXML_on_disk_ms2 <- readMSData(f, msLevel = 2, centroided. = FALSE, mode = "onDisk")
> 
> sf <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> sciex <- readMSData(sf, mode = "onDisk")
> 
> test_check("MSnbase")
Experiment data
  Experimenter name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Contact information: Laurent Gatto 
  Contact email: lg390@cam.ac.uk 
  Title: Example 'MSnExp' data set 
  URL:  
  PMIDs:  
  No abstract available.
Instrument : 
  Model: test (1) 
  Manufacturer:  
  Customisations:  
  Use 'msInfo(object)' for more MIAPE-MS information.
Experiment data
  Experimenter name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Contact information: Laurent Gatto 
  Contact email: lg390@cam.ac.uk 
  Title: Example 'MSnExp' data set 
  URL:  
  PMIDs:  
  No abstract available.
  notes:
   Note1:
First note
MIAPE-MS information:
 1. General features:
  Date stamp:  
  Contact: Laurent Gatto 
  Name: Laurent Gatto 
  Laboratory: Cambridge Centre for Proteomics (CCP) 
  Instument model: test 
  Manufacturer:  
  Customisations:  
  Software:  
  Version:  
  Switching:  
  Param file:  
 2. Ion source
  Source:  
  Source details:  
 3. Post-source componentry
  Analyzer:  
  Analyzer details:  
  Collision gas:  
  Pressure:   bars
  Energy:  
  Detector type:  
  Sensitivity:  
1
Object of class "MSmap"
 Map [75, 401]
  [1]  Retention time: 30:1 - 34:58 
  [2]  M/Z: 521 - 523 (res 0.005)
Object of class "MSmap"
 Map [401, 75]
  [1]  M/Z: 521 - 523 (res 0.005)
  [2]  Retention time: 30:1 - 34:58 
1
1
1
1
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
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: 0.19 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 Oct 17 03:42:25 2018] 
 MSnbase version: 2.6.4 
- - - 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: F1.S001 F1.S002 ... F1.S509 (509 total)
  fvarLabels: fileIdx spIdx ... spectrum (29 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 
MSn experiment data ("MSnExp")
Object size in memory: 0.17 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 5 
 MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 17 03:48:57 2018 
 MSnbase version: 2.6.4 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
  fvarLabels: spectrum
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
MSn experiment data ("MSnExp")
Object size in memory: 0.19 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 5 
 MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 17 03:48:58 2018 
 MSnbase version: 2.6.4 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
  fvarLabels: spectrum
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
1
Object of class "FeaturesOfInterest"
 Created on Wed Oct 17 03:49:22 2018 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Wed Oct 17 03:49:22 2018 
 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.
reading dummyiTRAQ.mzid... DONE!
Iterations of EM: 
1...2...3...4...5...6...7...8...9...10...11...
[1] 0.07947339
....== testthat results  ===========================================================
OK: 2012 SKIPPED: 8 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 491.92   34.14  668.35


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 2.6.4 
  Visit https://lgatto.github.io/MSnbase/ 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
> 
> ## Erwinia
> f <- msdata::proteomics(full.names = TRUE,
+                         pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
> tmt_erwinia_in_mem_ms1 <- readMSData(f, msLevel = 1)
> tmt_erwinia_in_mem_ms2 <- readMSData(f, msLevel = 2)
> tmt_erwinia_on_disk <- readMSData(f, mode = "onDisk")
> tmt_erwinia_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk")
> tmt_erwinia_on_disk_ms2 <- readMSData(f, msLevel = 2, mode = "onDisk")
> ## subset by rt
> tmt_im_ms1_sub <- filterRt(tmt_erwinia_in_mem_ms1, c(1200, 1250))
> tmt_im_ms2_sub <- filterRt(tmt_erwinia_in_mem_ms2, c(1200, 1250))
> tmt_od_sub <- filterRt(tmt_erwinia_on_disk, c(1200, 1250))
> tmt_od_ms1_sub <- filterRt(tmt_erwinia_on_disk_ms1, c(1200, 1250))
> tmt_od_ms2_sub <- filterRt(tmt_erwinia_on_disk_ms2, c(1200, 1250))
> 
> ## microtofq
> f <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+        system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_in_mem_ms1 <- readMSData(f, msLevel = 1)
> microtofq_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk")
> microtofq_on_disk <- readMSData(f, mode = "onDisk")
> 
> ## extdata mzML
> f <- dir(system.file(package = "MSnbase", dir = "extdata"),
+          full.name = TRUE, pattern = "mzXML$")
> extdata_mzXML_in_mem_ms2 <- readMSData(f, verbose = FALSE, centroided. = FALSE)
> extdata_mzXML_on_disk <- readMSData(f, centroided. = FALSE, mode = "onDisk")
> extdata_mzXML_on_disk_ms2 <- readMSData(f, msLevel = 2, centroided. = FALSE, mode = "onDisk")
> 
> sf <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> sciex <- readMSData(sf, mode = "onDisk")
> 
> 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:  
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
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.
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.23 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 Oct 17 03:53:40 2018] 
 MSnbase version: 2.6.4 
- - - 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: F1.S001 F1.S002 ... F1.S509 (509 total)
  fvarLabels: fileIdx spIdx ... spectrum (29 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 
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 Oct 17 04:00:15 2018 
 MSnbase version: 2.6.4 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
  fvarLabels: spectrum
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
MSn experiment data ("MSnExp")
Object size in memory: 0.21 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 5 
 MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 17 04:00:16 2018 
 MSnbase version: 2.6.4 
- - - Meta data  - - -
phenoData
  rowNames: dummyiTRAQ.mzXML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  dummyiTRAQ.mzXML 
protocolData: none
featureData
  featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
  fvarLabels: spectrum
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
1
Object of class "FeaturesOfInterest"
 Created on Wed Oct 17 04:00:41 2018 
 Description:
  small foi
 3 features of interest:
   P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
 Created on Wed Oct 17 04:00:41 2018 
 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.
reading dummyiTRAQ.mzid... DONE!
Iterations of EM: 
1...2...3...4...5...6...7...8...9...10...11...
[1] 0.07947339
....== testthat results  ===========================================================
OK: 2012 SKIPPED: 8 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 521.76   29.12  679.75

name	user	system	elapsed
Chromatogram-class	0.05	0.00	0.04
Chromatograms-class	0.22	0.00	0.22
FeatComp-class	0.33	0.03	0.61
FeaturesOfInterest-class	0.07	0.00	0.08
MSmap-class	0	0	0
MSnExp-class	0.63	0.00	0.70
MSnProcess-class	0	0	0
MSnSet-class	9.18	0.17	9.38
MSnSetList-class	3.36	0.34	3.70
MzTab-class	4.46	0.11	5.95
NAnnotatedDataFrame-class	0.02	0.00	0.02
OnDiskMSnExp-class	8.38	0.49	16.43
ProcessingStep-class	0.01	0.00	0.02
ReporterIons-class	0.02	0.00	0.02
TMT6	0	0	0
addIdentificationData-methods	0.83	0.00	0.99
aggvar	4.59	0.04	5.00
averageMSnSet	4.69	0.41	7.18
bin-methods	0.42	0.00	0.42
calculateFragments-methods	1.12	0.00	1.13
chromatogram-MSnExp-method	7.99	0.48	31.62
clean-methods	0.22	0.00	0.22
combineFeatures	1.11	0.02	1.12
combineSpectra	0.03	0.00	0.04
combineSpectraMovingWindow	2.75	0.09	36.71
commonFeatureNames	0.42	0.05	0.47
compareSpectra-methods	0.19	0.00	0.19
estimateMzResolution	7.84	0.69	10.56
estimateMzScattering	19.63	0.12	22.13
estimateNoise-method	0.01	0.00	0.01
exprsToRatios-methods	0.05	0.00	0.05
extractPrecSpectra-methods	0.84	0.00	0.84
factorsAsStrings	0.02	0.00	0.02
featureCV	0.01	0.00	0.02
fillUp	0	0	0
formatRt	0	0	0
get.amino.acids	0	0	0
get.atomic.mass	0	0	0
getVariableName	0	0	0
iPQF	0.20	0.02	0.22
iTRAQ4	0	0	0
imageNA2	2.67	0.12	2.79
impute-methods	0.46	0.05	0.62
isCentroidedFromFile	3.16	0.28	3.41
itraqdata	0.07	0.02	0.09
listOf	0	0	0
makeCamelCase	0	0	0
makeNaData	1.07	0.03	1.09
missing-data	2.46	0.10	2.55
mzRident2dfr	0.02	0.00	0.02
nFeatures	0.92	0.00	0.93
nQuants	0.11	0.01	0.13
naplot	0.08	0.02	0.09
navMS	2.65	0.14	34.39
normToReference	0.31	0.02	0.33
normalise-methods	0.02	0.00	0.02
npcv	0.02	0.00	0.01
pSet-class	0	0	0
pickPeaks-method	0.37	0.00	0.38
plot-methods	4.30	0.03	8.83
plot2d-methods	0.72	0.00	0.72
plotDensity-methods	0.73	0.00	0.73
plotMzDelta-methods	0.63	0.00	0.62
plotNA-methods	0.43	0.00	0.44
plotSpectrumSpectrum-methods	1.27	0.01	1.28
precSelection	0.01	0.00	0.02
purityCorrect-methods	0.04	0.00	0.03
quantify-methods	1.57	0.03	9.36
readMSData	1.60	0.02	1.60
readMSnSet	0.09	0.00	1.07
readMgfData	2.03	0.03	2.28
readMzIdData	1.48	0.14	3.97
readMzTabData	6.66	0.03	6.86
readMzTabData_v0.9	0.20	0.00	0.28
readSRMData	1.44	0.14	1.80
reduce-data.frame-method	0.02	0.00	0.02
removeNoId-methods	0.96	0.00	0.96
removePeaks-methods	0.55	0.01	0.57
removeReporters-methods	0.58	0.00	0.58
selectFeatureData	1.11	0.07	1.60
smooth-methods	0.20	0.00	0.21
trimMz-methods	0.19	0.00	0.19
writeMgfData-methods	0	0	0

name	user	system	elapsed
Chromatogram-class	0.04	0.00	0.11
Chromatograms-class	0.33	0.00	0.33
FeatComp-class	0.28	0.02	0.30
FeaturesOfInterest-class	0.06	0.00	0.06
MSmap-class	0	0	0
MSnExp-class	0.5	0.0	0.5
MSnProcess-class	0	0	0
MSnSet-class	9.55	0.19	13.20
MSnSetList-class	3.50	0.03	3.54
MzTab-class	3.83	0.01	4.27
NAnnotatedDataFrame-class	0.07	0.00	0.06
OnDiskMSnExp-class	8.51	0.35	8.86
ProcessingStep-class	0	0	0
ReporterIons-class	0.02	0.00	0.01
TMT6	0.01	0.00	0.02
addIdentificationData-methods	0.69	0.00	0.69
aggvar	4.20	0.00	4.34
averageMSnSet	5.25	0.23	10.36
bin-methods	0.49	0.00	0.49
calculateFragments-methods	1.47	0.00	1.47
chromatogram-MSnExp-method	11.55	0.58	35.67
clean-methods	0.20	0.01	0.22
combineFeatures	1.53	0.07	1.59
combineSpectra	0.05	0.00	0.05
combineSpectraMovingWindow	3.34	0.06	3.40
commonFeatureNames	0.25	0.03	0.28
compareSpectra-methods	0.17	0.00	0.18
estimateMzResolution	6.41	0.28	6.65
estimateMzScattering	16.96	0.10	17.06
estimateNoise-method	0.01	0.00	0.08
exprsToRatios-methods	0.10	0.00	0.09
extractPrecSpectra-methods	1.15	0.00	1.16
factorsAsStrings	0.01	0.00	0.02
featureCV	0.02	0.00	0.02
fillUp	0.01	0.00	0.01
formatRt	0	0	0
get.amino.acids	0	0	0
get.atomic.mass	0	0	0
getVariableName	0.02	0.00	0.02
iPQF	0.23	0.00	0.23
iTRAQ4	0.02	0.00	0.02
imageNA2	2.94	0.01	2.95
impute-methods	0.50	0.00	0.56
isCentroidedFromFile	3.58	0.20	3.77
itraqdata	0.04	0.02	0.06
listOf	0	0	0
makeCamelCase	0	0	0
makeNaData	0.89	0.00	0.89
missing-data	3.76	0.00	3.76
mzRident2dfr	0.05	0.00	0.05
nFeatures	1.11	0.03	1.14
nQuants	0.19	0.00	0.19
naplot	0.13	0.00	0.13
navMS	3.06	0.08	3.14
normToReference	0.36	0.00	0.36
normalise-methods	0.03	0.00	0.03
npcv	0	0	0
pSet-class	0.02	0.00	0.01
pickPeaks-method	0.43	0.01	0.46
plot-methods	4.40	0.05	4.44
plot2d-methods	0.85	0.00	0.85
plotDensity-methods	1.11	0.00	1.11
plotMzDelta-methods	0.94	0.00	0.94
plotNA-methods	0.67	0.00	0.67
plotSpectrumSpectrum-methods	1.5	0.0	1.5
precSelection	0.02	0.00	0.02
purityCorrect-methods	0.03	0.00	0.03
quantify-methods	2.36	0.02	10.94
readMSData	2.44	0.00	2.44
readMSnSet	0.13	0.00	0.13
readMgfData	2.47	0.01	2.49
readMzIdData	1.33	0.33	1.65
readMzTabData	5.58	0.05	5.75
readMzTabData_v0.9	0.19	0.01	0.25
readSRMData	1.44	0.11	1.54
reduce-data.frame-method	0.02	0.00	0.02
removeNoId-methods	1.16	0.00	1.15
removePeaks-methods	0.64	0.00	0.64
removeReporters-methods	0.64	0.00	0.64
selectFeatureData	1.12	0.00	1.13
smooth-methods	0.22	0.00	0.22
trimMz-methods	0.16	0.00	0.15
writeMgfData-methods	0	0	0

CHECK report for MSnbase on tokay2

Summary

Command output

Installation output

Tests output

Example timings