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

This page was generated on 2021-07-30 15:06:14 -0400 (Fri, 30 Jul 2021).

CHECK 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: 2021-07-29 04:50:02 -0400 (Thu, 29 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:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantFiltering.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VariantFiltering_1.28.0.tar.gz
StartedAt: 2021-07-30 07:26:49 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 07:38:25 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 696.9 seconds
RetCode: 0
Status:   OK  
CheckDir: VariantFiltering.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantFiltering.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VariantFiltering_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/VariantFiltering.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VariantFiltering/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantFiltering' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'VariantFiltering' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   3.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs'
  'VariantAnnotation:::.consolidateHits'
  'VariantAnnotation:::.returnEmpty'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.adjustForStrandSense' '.ancestorsSO' '.findSOIDs'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/VariantFiltering/libs/i386/VariantFiltering.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/VariantFiltering/libs/x64/VariantFiltering.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
VariantFilteringParam-class 9.05   4.68   18.27
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
VariantFilteringParam-class 8.61   3.13   11.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/VariantFiltering.Rcheck/00check.log'
for details.



Installation output

VariantFiltering.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
 25 3211k   25  804k    0     0  3923k      0 --:--:-- --:--:-- --:--:-- 3923k
100 3211k  100 3211k    0     0  7751k      0 --:--:-- --:--:-- --:--:-- 7756k

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

Tests output

VariantFiltering.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("VariantFiltering")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Assuming the genome build of the input variants is hs37d5.
Switching to the UCSC chromosome-name style from the transcript-centric annotation package.
Chromosome chrM has different lengths between the input VCF and the input TxDb pakage. This chromosome will be discarded from further analysis
Assumming hs37d5 and hg19 represent the same genome build.
Discarding scaffold sequences.
Annotating variant type (SNV, Insertion, Deletion, MNV, Delins)
Annotating location with VariantAnnotation::locateVariants()
Annotating coding variants VariantAnnotation::predictCoding()
Annotating codon usage frequencies in coding synonymous variants
Scoring binding sites with weight matrix donorSites.
Scoring binding sites with weight matrix acceptorSites.
1000 variants processed


RUNIT TEST PROTOCOL -- Fri Jul 30 07:36:29 2021 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VariantFiltering RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 597 out-of-bound ranges located on sequences
  29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
  72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
  73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
  76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
  sequence whose length is unknown (NA) or on a circular sequence are not
  considered out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying sequences). You can use
  trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
  information.
2: In annotationEngine(variants, param, annotationCache, BPPARAM = BPPARAM) :
  Assumming GRCh37.p13 and hs37d5 represent the same genome build.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 597 out-of-bound ranges located on sequences
  29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
  72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
  73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
  76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
  sequence whose length is unknown (NA) or on a circular sequence are not
  considered out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying sequences). You can use
  trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
  information.
4: In .scoreBindingSiteVariants(variantsVR_annotated, weightMatrices,  :
  Assumming GRCh37.p13 and hs37d5 represent the same genome build.
5: In recycleSingleBracketReplacementValue(value, x, nsbs) :
  number of values supplied is not a sub-multiple of the number of values to be replaced
6: In recycleSingleBracketReplacementValue(value, x, nsbs) :
  number of values supplied is not a sub-multiple of the number of values to be replaced
> 
> proc.time()
   user  system elapsed 
 100.29    9.75  123.98 

VariantFiltering.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("VariantFiltering")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Assuming the genome build of the input variants is hs37d5.
Switching to the UCSC chromosome-name style from the transcript-centric annotation package.
Chromosome chrM has different lengths between the input VCF and the input TxDb pakage. This chromosome will be discarded from further analysis
Assumming hs37d5 and hg19 represent the same genome build.
Discarding scaffold sequences.
Annotating variant type (SNV, Insertion, Deletion, MNV, Delins)
Annotating location with VariantAnnotation::locateVariants()
Annotating coding variants VariantAnnotation::predictCoding()
Annotating codon usage frequencies in coding synonymous variants
Scoring binding sites with weight matrix donorSites.
Scoring binding sites with weight matrix acceptorSites.
1000 variants processed


RUNIT TEST PROTOCOL -- Fri Jul 30 07:38:15 2021 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VariantFiltering RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 597 out-of-bound ranges located on sequences
  29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
  72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
  73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
  76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
  sequence whose length is unknown (NA) or on a circular sequence are not
  considered out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying sequences). You can use
  trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
  information.
2: In annotationEngine(variants, param, annotationCache, BPPARAM = BPPARAM) :
  Assumming GRCh37.p13 and hs37d5 represent the same genome build.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 597 out-of-bound ranges located on sequences
  29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
  72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
  73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
  76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
  sequence whose length is unknown (NA) or on a circular sequence are not
  considered out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying sequences). You can use
  trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
  information.
4: In .scoreBindingSiteVariants(variantsVR_annotated, weightMatrices,  :
  Assumming GRCh37.p13 and hs37d5 represent the same genome build.
5: In recycleSingleBracketReplacementValue(value, x, nsbs) :
  number of values supplied is not a sub-multiple of the number of values to be replaced
6: In recycleSingleBracketReplacementValue(value, x, nsbs) :
  number of values supplied is not a sub-multiple of the number of values to be replaced
> 
> proc.time()
   user  system elapsed 
  95.90    7.46  105.64 

Example timings

VariantFiltering.Rcheck/examples_i386/VariantFiltering-Ex.timings

nameusersystemelapsed
GenePhylostrataDb-class000
VariantFilteringParam-class 9.05 4.6818.27
VariantFilteringResults-class000
VariantType-class000
WeightMatrix-class0.030.000.12
autosomalDominant000
autosomalRecessiveHeterozygous000
autosomalRecessiveHomozygous0.020.000.02
deNovo000
readAAradicalChangeMatrix000
unrelatedIndividuals000
xLinked000

VariantFiltering.Rcheck/examples_x64/VariantFiltering-Ex.timings

nameusersystemelapsed
GenePhylostrataDb-class000
VariantFilteringParam-class 8.61 3.1311.91
VariantFilteringResults-class000
VariantType-class000
WeightMatrix-class0.020.000.02
autosomalDominant000
autosomalRecessiveHeterozygous000
autosomalRecessiveHomozygous000
deNovo000
readAAradicalChangeMatrix000
unrelatedIndividuals000
xLinked000