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

This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).

INSTALL results for genoset on tokay2

To the developers/maintainers of the genoset package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genoset.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 750/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.48.0  (landing page)
Peter M. Haverty
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/genoset
git_branch: RELEASE_3_13
git_last_commit: 6006c44
git_last_commit_date: 2021-05-19 11:48:08 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: genoset
Version: 1.48.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/genoset_1.48.0.tar.gz && rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoset.buildbin-libdir genoset_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL genoset_1.48.0.zip && rm genoset_1.48.0.tar.gz genoset_1.48.0.zip
StartedAt: 2021-10-14 08:54:09 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 08:55:37 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 87.8 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/genoset_1.48.0.tar.gz && rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoset.buildbin-libdir genoset_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL genoset_1.48.0.zip && rm genoset_1.48.0.tar.gz genoset_1.48.0.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
100  108k  100  108k    0     0   566k      0 --:--:-- --:--:-- --:--:--  569k

install for i386

* installing *source* package 'genoset' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bounds.c -o bounds.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rangeSummaries.c -o rangeSummaries.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utils.c -o utils.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.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/genoset.buildbin-libdir/00LOCK-genoset/00new/genoset/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genoset'
    finding HTML links ... done
    GenoSet-class                           html  
    finding level-2 HTML links ... done

    RleDataFrame-class                      html  
    RleDataFrame-views                      html  
    baf2mbaf                                html  
    boundingIndices                         html  
    boundingIndicesByChr                    html  
    bounds2Rle                              html  
    calcGC                                  html  
    calcGC2                                 html  
    chr-methods                             html  
    chrIndices-methods                      html  
    chrInfo-methods                         html  
    chrNames-methods                        html  
    chrOrder                                html  
    chrPartitioning                         html  
    cn2lr-methods                           html  
    do_rledf_range_summary                  html  
    do_rledf_views                          html  
    fixSegNAs                               html  
    gcCorrect                               html  
    genoPlot-methods                        html  
    genoPos-methods                         html  
    genome                                  html  
    genomeAxis                              html  
    genomicranges-methods                   html  
    genoset-dataset                         html  
    genoset-methods                         html  
    genoset-package                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/genoset.buildbin-libdir/00LOCK-genoset/00new/genoset/help/genoset.html
    genoset-subset                          html  
    isGenomeOrder                           html  
    lr2cn                                   html  
    modeCenter                              html  
    numCallable                             html  
    pos-methods                             html  
    rangeSampleMeans                        html  
    rangeSegMeanLength-methods              html  
    rbindDataframe                          html  
    readGenoSet                             html  
    runCBS                                  html  
    segPairTable-methods                    html  
    segTable-methods                        html  
    segs2Granges                            html  
    segs2Rle                                html  
    segs2RleDataFrame                       html  
    toGenomeOrder                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'genoset' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'genoset' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'genoset' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bounds.c -o bounds.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rangeSummaries.c -o rangeSummaries.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utils.c -o utils.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.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/genoset.buildbin-libdir/genoset/libs/x64
** testing if installed package can be loaded
Warning: Package 'genoset' is deprecated and will be removed from Bioconductor
  version 3.14
* MD5 sums
packaged installation of 'genoset' as genoset_1.48.0.zip
* DONE (genoset)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'genoset' successfully unpacked and MD5 sums checked