Back to "Blame Jeroen" build/check report for BioC 3.11

INSTALL report for MSnbase on tokay2

This page was generated on 2020-04-15 03:20:15 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE MSnbase PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 55/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.13.6
Laurent Gatto
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/MSnbase
Branch: master
Last Commit: 6d41fd1
Last Changed Date: 2020-04-14 10:17:32 -0400 (Tue, 14 Apr 2020)
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] ERROR  skipped  skipped 

Summary

Package: MSnbase
Version: 2.13.6
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/MSnbase_2.13.6.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.13.6.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL MSnbase_2.13.6.zip && rm MSnbase_2.13.6.tar.gz MSnbase_2.13.6.zip
StartedAt: 2020-04-14 18:16:07 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:17:44 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 96.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/MSnbase_2.13.6.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.13.6.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL MSnbase_2.13.6.zip && rm MSnbase_2.13.6.tar.gz MSnbase_2.13.6.zip
###
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100 1782k  100 1782k    0     0  10.7M      0 --:--:-- --:--:-- --:--:-- 11.1M

install for i386

* installing *source* package 'MSnbase' ...
** using staged installation
** libs
/mingw32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
             ^~~~~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
             ^~~~~~~~~~~~~~
/mingw32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                  ^~~
At top level:
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)
            ^~~~~~~~~~~~~~~~~~~~~~~~
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)
            ^~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/g++ -std=gnu++11 -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/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/libs/i386
** R
** data
*** moving datasets to lazyload DB
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 '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  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatogram-class.Rd:142: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatogram-class.Rd:146: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatogram-class.Rd:156: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    Chromatograms-class                     html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatograms-class.Rd:145: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatograms-class.Rd:150: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/MSnExp-class.Rd:252: 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/MSnSet-class.Rd:504: 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  
    OnDiskMSnExp-class                      html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/OnDiskMSnExp-class.Rd:509: file link 'normalize' in package 'MSnbase' does not exist and so has been treated as a topic
    ProcessingStep-class                    html  
    ReporterIons-class                      html  
    Spectra                                 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/chromatogram-MSnExp-method.Rd:76: 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/combineFeatures.Rd:44: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/combineFeatures.Rd:151: 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  
    consensusSpectrum                       html  
    defunct                                 html  
    estimateMzResolution                    html  
    estimateMzScattering                    html  
    estimateNoise-method                    html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/estimateNoise-method.Rd:45: file link 'estimateNoise' in package 'MALDIquant' does not exist and so has been treated as a topic
    extractPrecSpectra-methods              html  
    fData-utils                             html  
    factorsAsStrings                        html  
    featureCV                               html  
    fillUp                                  html  
    filterIdentificationDataFrame           html  
    formatRt                                html  
    get.amino.acids                         html  
    get.atomic.mass                         html  
    getVariableName                         html  
    grepEcols                               html  
    hasSpectraOrChromatograms               html  
    iPQF                                    html  
    iTRAQ4                                  html  
    imageNA2                                html  
    impute-methods                          html  
    isCentroidedFromFile                    html  
    itraqdata                               html  
    listOf                                  html  
    makeCamelCase                           html  
    makeNaData                              html  
    meanMzInts                              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  
    writeMzTabData                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MSnbase' ...
** libs
/mingw64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
             ^~~~~~~~~~~~~~
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
             ^~~~~~~~~~~~~~
/mingw64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                  ^~~
At top level:
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)
            ^~~~~~~~~~~~~~~~~~~~~~~~
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)
            ^~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/g++ -std=gnu++11 -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/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_2.13.6.zip
* DONE (MSnbase)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'MSnbase' successfully unpacked and MD5 sums checked