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This page was generated on 2021-07-30 15:06:00 -0400 (Fri, 30 Jul 2021).

INSTALL results for MSnbase on tokay2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnbase.git to
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raw results

Package 1203/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.18.0  (landing page)
Laurent Gatto
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/MSnbase
Branch: RELEASE_3_13
Last Commit: 8653c08
Last Changed Date: 2021-05-19 11:47:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSnbase
Version: 2.18.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSnbase_2.18.0.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSnbase_2.18.0.zip && rm MSnbase_2.18.0.tar.gz MSnbase_2.18.0.zip
StartedAt: 2021-07-29 08:55:16 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 08:58:28 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 191.5 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSnbase_2.18.0.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSnbase_2.18.0.zip && rm MSnbase_2.18.0.tar.gz MSnbase_2.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1789k  100 1789k    0     0  3705k      0 --:--:-- --:--:-- --:--:-- 3712k

install for i386

* installing *source* package 'MSnbase' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/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,
             ^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/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,
             ^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/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)
            ^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/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/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/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  
    finding level-2 HTML links ... done

    FeatComp-class                          html  
    FeaturesOfInterest-class                html  
REDIRECT:topic	 names<-,FoICollection,character-method -> FeaturesOfInterest-class.html [ FAIL ]
    MChromatograms-class                    html  
REDIRECT:topic	 [<-,MChromatograms-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 pData<-,MChromatograms,data.frame-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 $<-,MChromatograms-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 colnames<-,MChromatograms-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 sampleNames<-,MChromatograms,ANY-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 featureNames<-,MChromatograms-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 featureData<-,MChromatograms,ANY-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 fData<-,MChromatograms,ANY-method -> MChromatograms-class.html [ FAIL ]
REDIRECT:topic	 rownames<-,MChromatograms-method -> MChromatograms-class.html [ FAIL ]
    MIAPE-class                             html  
REDIRECT:topic	 class:MIAPE -> MIAPE-class.html [ FAIL ]
REDIRECT:topic	 pubMedIds<-,MIAPE-method -> MIAPE-class.html [ FAIL ]
REDIRECT:topic	 notes<-,MIAPE-method -> MIAPE-class.html [ FAIL ]
    MSmap-class                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/help/msMap.html
    MSnExp-class                            html  
REDIRECT:topic	 class:MSnExp -> MSnExp-class.html [ FAIL ]
    MSnProcess-class                        html  
REDIRECT:topic	 class:MSnProcess -> MSnProcess-class.html [ FAIL ]
    MSnSet-class                            html  
REDIRECT:topic	 class:MSnSet -> MSnSet-class.html [ FAIL ]
REDIRECT:topic	 experimentData<-,MSnSet,MIAPE-method -> MSnSet-class.html [ FAIL ]
REDIRECT:topic	 pData<-,MSnSet,data.frame-method -> MSnSet-class.html [ FAIL ]
REDIRECT:topic	 fData<-,MSnSet,data.frame-method -> MSnSet-class.html [ FAIL ]
    MSnSetList-class                        html  
REDIRECT:topic	 names<-,MSnSetList,ANY-method -> MSnSetList-class.html [ FAIL ]
REDIRECT:topic	 fData<-,MSnSetList,DataFrame-method -> MSnSetList-class.html [ FAIL ]
    MSnbaseOptions                          html  
    MSpectra                                html  
    MzTab-class                             html  
REDIRECT:topic	 class:MzTab -> MzTab-class.html [ FAIL ]
    OnDiskMSnExp-class                      html  
REDIRECT:topic	 class:OnDiskMSnExp -> OnDiskMSnExp-class.html [ FAIL ]
REDIRECT:topic	 centroided<-,OnDiskMSnExp,logical-method -> OnDiskMSnExp-class.html [ FAIL ]
REDIRECT:topic	 smoothed<-,OnDiskMSnExp,logical-method -> OnDiskMSnExp-class.html [ FAIL ]
REDIRECT:topic	 featureNames<-,OnDiskMSnExp-method -> OnDiskMSnExp-class.html [ FAIL ]
REDIRECT:topic	 featureNames<-,OnDiskMSnExp,ANY-method -> OnDiskMSnExp-class.html [ FAIL ]
    ProcessingStep-class                    html  
REDIRECT:topic	 ProcessingStep:OnDiskMSnExp -> ProcessingStep-class.html [ FAIL ]
    ReporterIons-class                      html  
REDIRECT:topic	 class:ReporterIons -> ReporterIons-class.html [ FAIL ]
REDIRECT:topic	 reporterNames<-,ReporterIons-method -> ReporterIons-class.html [ FAIL ]
REDIRECT:topic	 reporterNames<-,ReporterIons,ANY-method -> ReporterIons-class.html [ FAIL ]
REDIRECT:topic	 reporterNames<-,ReporterIons,character-method -> ReporterIons-class.html [ FAIL ]
REDIRECT:topic	 reporterNames<- -> ReporterIons-class.html [ FAIL ]
    Spectrum-class                          html  
REDIRECT:topic	 class:Spectrum -> Spectrum-class.html [ FAIL ]
REDIRECT:topic	 centroided<-,Spectrum,ANY-method -> Spectrum-class.html [ FAIL ]
REDIRECT:topic	 centroided<-,Spectrum,logical-method -> Spectrum-class.html [ FAIL ]
REDIRECT:topic	 centroided<- -> Spectrum-class.html [ FAIL ]
REDIRECT:topic	 smoothed<-,Spectrum,ANY-method -> Spectrum-class.html [ FAIL ]
REDIRECT:topic	 smoothed<-,Spectrum,logical-method -> Spectrum-class.html [ FAIL ]
REDIRECT:topic	 smoothed<- -> Spectrum-class.html [ FAIL ]
    Spectrum1-class                         html  
REDIRECT:topic	 class:Spectrum1 -> Spectrum1-class.html [ FAIL ]
    Spectrum2-class                         html  
REDIRECT:topic	 class:Spectrum2 -> Spectrum2-class.html [ FAIL ]
    TMT6                                    html  
    addIdentificationData-methods           html  
    aggvar                                  html  
    averageMSnSet                           html  
    bin-methods                             html  
    calculateFragments-methods              html  
    chromatogram-MSnExp-method              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/help/chromatogram.html
    clean-methods                           html  
    combineFeatures                         html  
    combineSpectra                          html  
    combineSpectraMovingWindow              html  
    commonFeatureNames                      html  
    compareMSnSets                          html  
    compareSpectra-methods                  html  
    consensusSpectrum                       html  
    defunct                                 html  
REDIRECT:topic	 class:NAnnotatedDataFrame -> defunct.html [ FAIL ]
    estimateMzResolution                    html  
    estimateMzScattering                    html  
    estimateNoise-method                    html  
    extractPrecSpectra-methods              html  
    extractSpectraData                      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                                  html  
    isCentroidedFromFile                    html  
    itraqdata                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/help/msnset.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  
REDIRECT:topic	 class:pSet -> pSet-class.html [ FAIL ]
REDIRECT:topic	 $<-,pSet-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 fData<-,pSet,data.frame-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 centroided<-,pSet,ANY-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 centroided<-,pSet,logical-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 smoothed<-,pSet,ANY-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 smoothed<-,pSet,logical-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 pData<-,pSet,ANY-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 phenoData<-,pSet,ANY-method -> pSet-class.html [ FAIL ]
REDIRECT:topic	 sampleNames<-,pSet,character-method -> pSet-class.html [ FAIL ]
    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
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/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,
             ^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/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,
             ^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/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)
            ^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/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/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_2.18.0.zip
* DONE (MSnbase)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MSnbase' successfully unpacked and MD5 sums checked