Back to Multiple platform build/check report for BioC 3.13
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-22 15:05:16 -0400 (Wed, 22 Sep 2021).

INSTALL results for genomation on tokay2

To the developers/maintainers of the genomation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomation.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 735/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomation 1.24.0  (landing page)
Altuna Akalin , Vedran Franke
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/genomation
git_branch: RELEASE_3_13
git_last_commit: 94f0278
git_last_commit_date: 2021-05-19 12:09:55 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: genomation
Version: 1.24.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/genomation_1.24.0.tar.gz && rm -rf genomation.buildbin-libdir && mkdir genomation.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genomation.buildbin-libdir genomation_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL genomation_1.24.0.zip && rm genomation_1.24.0.tar.gz genomation_1.24.0.zip
StartedAt: 2021-09-21 10:16:09 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 10:17:47 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 98.4 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/genomation_1.24.0.tar.gz && rm -rf genomation.buildbin-libdir && mkdir genomation.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genomation.buildbin-libdir genomation_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL genomation_1.24.0.zip && rm genomation_1.24.0.tar.gz genomation_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  3 4092k    3  155k    0     0   730k      0  0:00:05 --:--:--  0:00:05  729k
 75 4092k   75 3090k    0     0  2548k      0  0:00:01  0:00:01 --:--:-- 2547k
100 4092k  100 4092k    0     0  2066k      0  0:00:01  0:00:01 --:--:-- 2066k

install for i386

* installing *source* package 'genomation' ...
** 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/"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 binSum.cpp -o binSum.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o binSum.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/genomation.buildbin-libdir/00LOCK-genomation/00new/genomation/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** help
*** installing help indices
  converting help for package 'genomation'
    finding HTML links ... done
    AnnotationByFeature-class               html  
    AnnotationByGeneParts-class             html  
    AnnotationByGeneParts-methods           html  
    Max_c                                   html  
    Mean_c                                  html  
    Median_c                                html  
    Min_c                                   html  
    Ops-ScoreMatrix-ScoreMatrix-method      html  
    Ops-ScoreMatrixList-ScoreMatrixList-method
                                            html  
    Ops-ScoreMatrixList-numeric-method      html  
    Ops-numeric-ScoreMatrixList-method      html  
    RandomEnrichment-class                  html  
    ScoreMatrix-class                       html  
    ScoreMatrix-methods                     html  
    ScoreMatrixBin-methods                  html  
    ScoreMatrixList-class                   html  
    ScoreMatrixList-methods                 html  
    Sum_c                                   html  
    annotatGrWithGeneParts                  html  
    annotateWithFeature-methods             html  
    annotateWithFeatureFlank-methods        html  
    annotateWithFeatures-methods            html  
    annotateWithGeneParts-methods           html  
    finding level-2 HTML links ... done

    bed12ToExons                            html  
    bed12ToIntrons                          html  
    binMatrix-methods                       html  
    binMax                                  html  
    binMean                                 html  
    binMedian                               html  
    binMin                                  html  
    binSum                                  html  
    binner                                  html  
    c.ScoreMatrix                           html  
    c.ScoreMatrixList                       html  
    cage                                    html  
    calculateOverlapSignificance-methods    html  
    checkBedValidity                        html  
    checkClass                              html  
    compressedAndUrl2temp                   html  
    constrainRanges                         html  
    convertBed2Exons-methods                html  
    convertBed2Introns-methods              html  
    convertBedDf-methods                    html  
    cpgi                                    html  
    detectUCSCheader                        html  
    distance2NearestFeature                 html  
    enrichmentMatrix-ScoreMatrix-method     html  
    enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method
                                            html  
    enrichmentMatrix-ScoreMatrixList-method
                                            html  
    file.ext                                html  
    findFeatureComb-methods                 html  
    galpTo2Ranges                           html  
    genes                                   html  
    getColors                               html  
    getFeatsWithTargetsStats-methods        html  
    getFlanks-methods                       html  
    getMembers-methods                      html  
    getRandomEnrichment-methods             html  
    getTargetAnnotationStats-methods        html  
    gffToGRanges                            html  
    heatMatrix                              html  
    heatMeta                                html  
    heatTargetAnnotation-methods            html  
    intersectScoreMatrixList-methods        html  
    listSliceMax                            html  
    listSliceMean                           html  
    listSliceMedian                         html  
    listSliceMin                            html  
    listSliceSum                            html  
    multiHeatMatrix                         html  
    orderBy-methods                         html  
    patternMatrix-methods                   html  
    plotMeta                                html  
    plotTargetAnnotation-methods            html  
    promoters                               html  
    randomizeFeature-methods                html  
    read.zip                                html  
    readBam                                 html  
    readBed                                 html  
    readBigWig                              html  
    readBroadPeak                           html  
    readFeatureFlank-methods                html  
    readGeneric                             html  
    readNarrowPeak                          html  
    readTableFast                           html  
    readTranscriptFeatures-methods          html  
    scaleScoreMatrix-methods                html  
    scaleScoreMatrixList                    html  
    show-methods                            html  
    sub-ScoreMatrix-ANY-ANY-ANY-method      html  
    sub-ScoreMatrixList-ANY-ANY-ANY-method
                                            html  
    target.type                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'genomation' ...
** 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/"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 binSum.cpp -o binSum.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o binSum.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/genomation.buildbin-libdir/genomation/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
* MD5 sums
packaged installation of 'genomation' as genomation_1.24.0.zip
* DONE (genomation)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'genomation' successfully unpacked and MD5 sums checked