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This page was generated on 2022-04-13 12:06:09 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for AneuFinder on tokay2


To the developers/maintainers of the AneuFinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AneuFinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 54/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.22.0  (landing page)
Aaron Taudt
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/AneuFinder
git_branch: RELEASE_3_14
git_last_commit: ea0beb3
git_last_commit_date: 2021-10-26 12:26:30 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: AneuFinder
Version: 1.22.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AneuFinder_1.22.0.tar.gz && rm -rf AneuFinder.buildbin-libdir && mkdir AneuFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AneuFinder.buildbin-libdir AneuFinder_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AneuFinder_1.22.0.zip && rm AneuFinder_1.22.0.tar.gz AneuFinder_1.22.0.zip
StartedAt: 2022-04-12 05:49:08 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 05:52:50 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 221.6 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AneuFinder_1.22.0.tar.gz && rm -rf AneuFinder.buildbin-libdir && mkdir AneuFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AneuFinder.buildbin-libdir AneuFinder_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AneuFinder_1.22.0.zip && rm AneuFinder_1.22.0.tar.gz AneuFinder_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  188k  100  188k    0     0   236k      0 --:--:-- --:--:-- --:--:--  236k
100  188k  100  188k    0     0   236k      0 --:--:-- --:--:-- --:--:--  236k

install for i386

* installing *source* package 'AneuFinder' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c densities.cpp -o densities.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loghmm.cpp -o loghmm.o
loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility.cpp -o utility.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/AneuFinder.buildbin-libdir/00LOCK-AneuFinder/00new/AneuFinder/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AneuFinder'
    finding HTML links ... done
    AneuFinder-package                      html  
    Aneufinder                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/AneuFinder.buildbin-libdir/00LOCK-AneuFinder/00new/AneuFinder/help/Aneufinder.html
    finding level-2 HTML links ... done

    DNAcopy.findCNVs                        html  
    HMM.findCNVs                            html  
    aneuBiHMM                               html  
    aneuHMM                                 html  
    annotateBreakpoints                     html  
    bam2GRanges                             html  
    bed2GRanges                             html  
    bi.edivisive.findCNVs                   html  
    biDNAcopy.findCNVs                      html  
    biHMM.findCNVs                          html  
    binReads                                html  
    binned.data                             html  
    binning                                 html  
    blacklist                               html  
    clusterByQuality                        html  
    clusterHMMs                             html  
    collapseBins                            html  
    colors                                  html  
    compareMethods                          html  
    compareModels                           html  
    consensusSegments                       html  
    correctGC                               html  
    edivisive.findCNVs                      html  
    estimateComplexity                      html  
    export                                  html  
    filterSegments                          html  
    findCNVs                                html  
    findCNVs.strandseq                      html  
    findHotspots                            html  
    fixedWidthBins                          html  
    getBreakpoints                          html  
    getDistinctColors                       html  
    getQC                                   html  
    getSCEcoordinates                       html  
    heatmapAneuploidies                     html  
    heatmapGenomewide                       html  
    heatmapGenomewideClusters               html  
    hotspotter                              html  
    hotspotter.variable                     html  
    importBed                               html  
    initializeStates                        html  
    karyotypeMeasures                       html  
    loadFromFiles                           html  
    mergeStrandseqFiles                     html  
    plot.GRanges                            html  
    plot.GRangesList                        html  
    plot.aneuBiHMM                          html  
    plot.aneuHMM                            html  
    plot.character                          html  
    plotHeterogeneity                       html  
    plotHistogram                           html  
    plotKaryogram                           html  
    plotProfile                             html  
    plot_pca                                html  
    print.aneuBiHMM                         html  
    print.aneuHMM                           html  
    qualityControl                          html  
    readConfig                              html  
    refineBreakpoints                       html  
    simulateReads                           html  
    subsetByCNVprofile                      html  
    transCoord                              html  
    variableWidthBins                       html  
    writeConfig                             html  
    zinbinom                                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 'AneuFinder' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c densities.cpp -o densities.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loghmm.cpp -o loghmm.o
loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility.cpp -o utility.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/AneuFinder.buildbin-libdir/AneuFinder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AneuFinder' as AneuFinder_1.22.0.zip
* DONE (AneuFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'AneuFinder' successfully unpacked and MD5 sums checked