Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2021-07-23 15:06:25 -0400 (Fri, 23 Jul 2021).

INSTALL results for VariantFiltering on tokay2

To the developers/maintainers of the VariantFiltering package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantFiltering.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 1997/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.28.0  (landing page)
Robert Castelo
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/VariantFiltering
Branch: RELEASE_3_13
Last Commit: a7b2d16
Last Changed Date: 2021-05-19 12:04:28 -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: VariantFiltering
Version: 1.28.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/VariantFiltering_1.28.0.tar.gz && rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantFiltering.buildbin-libdir VariantFiltering_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.28.0.zip && rm VariantFiltering_1.28.0.tar.gz VariantFiltering_1.28.0.zip
StartedAt: 2021-07-22 11:14:01 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 11:15:49 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 108.1 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/VariantFiltering_1.28.0.tar.gz && rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantFiltering.buildbin-libdir VariantFiltering_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.28.0.zip && rm VariantFiltering_1.28.0.tar.gz VariantFiltering_1.28.0.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
  0 3211k    0  3835    0     0  69844      0  0:00:47 --:--:--  0:00:47 69727
100 3211k  100 3211k    0     0  5136k      0 --:--:-- --:--:-- --:--:-- 5137k

install for i386

* installing *source* package 'VariantFiltering' ...
** using staged installation
** libs
"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/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.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/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.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/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.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/VariantFiltering.buildbin-libdir/00LOCK-VariantFiltering/00new/VariantFiltering/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'VariantFiltering'
    finding HTML links ... done
    GenePhylostrataDb-class                 html  
    VariantFiltering-defunct                html  
    VariantFiltering-deprecated             html  
REDIRECT:topic	 dbSNPpresent<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 dbSNPpresent<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 dbSNPpresent<-,VariantFilteringResults,ANY-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantType<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantType<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantType<-,VariantFilteringResults,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantType<-,VariantFilteringResults,ANY,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantLocation<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantLocation<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantLocation<-,VariantFilteringResults,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantLocation<-,VariantFilteringResults,ANY,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantConsequence<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantConsequence<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantConsequence<-,VariantFilteringResults,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 variantConsequence<-,VariantFilteringResults,ANY,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 aaChangeType<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 aaChangeType<-,VariantFilteringResults,character-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 OMIMpresent<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 OMIMpresent<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 OMIMpresent<-,VariantFilteringResults,character-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 naMAF<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 naMAF<-,VariantFilteringResults,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 maxMAF<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 maxMAF<-,VariantFilteringResults,numeric-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 MAFpop<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 MAFpop<-,VariantFilteringResults,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 MAFpop<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 MAFpop<-,VariantFilteringResults,ANY,logical-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minPhastCons<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minPhastCons<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minPhastCons<-,VariantFilteringResults,ANY-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minPhylostratum<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minPhylostratum<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minPhylostratum<-,VariantFilteringResults,ANY-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minScore5ss<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minScore5ss<-,VariantFilteringResults,ANY-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minScore5ss<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minScore3ss<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minScore3ss<-,VariantFilteringResults,ANY-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minScore3ss<-,VariantFilteringResults-method -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minCUFC<- -> VariantFiltering-deprecated.html [ FAIL ]
REDIRECT:topic	 minCUFC<-,VariantFilteringResults,numeric-method -> VariantFiltering-deprecated.html [ FAIL ]
    finding level-2 HTML links ... done

    VariantFiltering-package                html  
    VariantFilteringParam-class             html  
REDIRECT:topic	 class:VariantFilteringParam -> VariantFilteringParam-class.html [ FAIL ]
    VariantFilteringResults-class           html  
REDIRECT:topic	 class:VariantFilteringResults -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 class:CutoffsList -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 filters<- -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 filters<-,VariantFilteringResults-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 cutoffs<- -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 cutoffs<-,VariantFilteringResults-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 cutoffs<-,VariantFilteringResults,CutoffsList-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 cutoffs<-,VariantFilteringResults,logical-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 change<- -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 change<-,CutoffsList -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 change<-,CutoffsList,ANY,integer-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 change<-,CutoffsList,ANY,numeric-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 change<-,CutoffsList,ANY,character-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 change<-,CutoffsList,ANY,logical-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 sortings<- -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 sortings<-,VariantFilteringResults,CutoffsList-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 softFilterMatrix<-,VariantFilteringResults-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 samples<- -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 samples<-,VariantFilteringResults-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 samples<-,VariantFilteringResults,character-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 bamFiles<- -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 bamFiles<-,VariantFilteringResults-method -> VariantFilteringResults-class.html [ FAIL ]
REDIRECT:topic	 bamFiles<-,VariantFilteringResults,BamViews-method -> VariantFilteringResults-class.html [ FAIL ]
    VariantType-class                       html  
REDIRECT:topic	 minIntronLength<- -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 minIntronLength<-,FiveSpliceSiteVariants-method -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 minIntronLength<-,ThreeSpliceSiteVariants-method -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 upstream<- -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 upstream<-,FiveSpliceSiteVariants-method -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 upstream<-,ThreeSpliceSiteVariants-method -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 downstream<- -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 downstream<-,FiveSpliceSiteVariants-method -> VariantType-class.html [ FAIL ]
REDIRECT:topic	 downstream<-,ThreeSpliceSiteVariants-method -> VariantType-class.html [ FAIL ]
    WeightMatrix-class                      html  
REDIRECT:topic	 wmLocations<-,WeightMatrix-method -> WeightMatrix-class.html [ FAIL ]
REDIRECT:topic	 wmLocations<-,WeightMatrix,character-method -> WeightMatrix-class.html [ FAIL ]
REDIRECT:topic	 wmStrictLocations<-,WeightMatrix-method -> WeightMatrix-class.html [ FAIL ]
REDIRECT:topic	 wmStrictLocations<-,WeightMatrix,logical-method -> WeightMatrix-class.html [ FAIL ]
REDIRECT:topic	 wmLocations<- -> WeightMatrix-class.html [ FAIL ]
REDIRECT:topic	 wmStrictLocations<- -> WeightMatrix-class.html [ FAIL ]
    autosomalDominant                       html  
    autosomalRecessiveHeterozygous          html  
    autosomalRecessiveHomozygous            html  
    deNovo                                  html  
    readAAradicalChangeMatrix               html  
    unrelatedIndividuals                    html  
    xLinked                                 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 'VariantFiltering' ...
** libs
"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/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.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/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.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/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.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/VariantFiltering.buildbin-libdir/VariantFiltering/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantFiltering' as VariantFiltering_1.28.0.zip
* DONE (VariantFiltering)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'VariantFiltering' successfully unpacked and MD5 sums checked