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CHECK report for GenomicFiles on tokay1

This page was generated on 2018-04-12 13:24:12 -0400 (Thu, 12 Apr 2018).

Package 565/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFiles 1.14.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GenomicFiles
Branch: RELEASE_3_6
Last Commit: 3b4831c
Last Changed Date: 2017-10-30 12:40:14 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicFiles
Version: 1.14.0
Command: rm -rf GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && mkdir GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFiles.buildbin-libdir GenomicFiles_1.14.0.tar.gz >GenomicFiles.Rcheck\00install.out 2>&1 && cp GenomicFiles.Rcheck\00install.out GenomicFiles-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicFiles.buildbin-libdir --install="check:GenomicFiles-install.out" --force-multiarch --no-vignettes --timings GenomicFiles_1.14.0.tar.gz
StartedAt: 2018-04-12 00:17:46 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:36:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 1112.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicFiles.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && mkdir GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFiles.buildbin-libdir GenomicFiles_1.14.0.tar.gz >GenomicFiles.Rcheck\00install.out 2>&1 && cp GenomicFiles.Rcheck\00install.out GenomicFiles-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicFiles.buildbin-libdir --install="check:GenomicFiles-install.out" --force-multiarch --no-vignettes --timings GenomicFiles_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFiles.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFiles/DESCRIPTION' ... OK
* this is package 'GenomicFiles' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'GenomicRanges' 'SummarizedExperiment' 'BiocParallel'
  'Rsamtools' 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GenomicFiles' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/GenomicFiles-class.Rd:111: missing file link 'SummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:77: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:97: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:128: missing file link 'VcfFileList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:129: missing file link 'VcfFileList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:132: missing file link 'seqinfo<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:138: missing file link 'seqlevelsStyle<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:142: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:147: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:154: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:162: missing file link 'genotypeToSnpMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:172: missing file link 'ScanVcfParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFileList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:12: missing file link 'BamFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:29: missing file link 'BamFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:121: missing file link 'BamFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:122: missing file link 'TabixFile'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFiles.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
VcfStack-class        4.44   0.02   31.92
reduceByYield         1.24   0.07   36.03
GenomicFiles-class    0.83   0.06   33.27
reduceByRange-methods 0.22   0.01   44.89
reduceByFile-methods  0.21   0.00   64.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
VcfStack-class        4.78   0.04   32.29
reduceByYield         1.84   0.08   25.09
GenomicFiles-class    1.61   0.03   32.94
reduceByRange-methods 0.28   0.02   55.82
reduceByFile-methods  0.30   0.00   65.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'GenomicFiles_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'GenomicFiles_unit_tests.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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFiles.Rcheck/00check.log'
for details.



Installation output

GenomicFiles.Rcheck/00install.out


install for i386

* installing *source* package 'GenomicFiles' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicFiles'
    finding HTML links ... done
    GenomicFiles-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/GenomicFiles-class.Rd:111: missing file link 'SummarizedExperiment'
    GenomicFiles-deprecated                 html  
    VcfStack-class                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:77: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:97: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:128: missing file link 'VcfFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:129: missing file link 'VcfFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:132: missing file link 'seqinfo<-'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:138: missing file link 'seqlevelsStyle<-'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:142: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:147: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:154: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:162: missing file link 'genotypeToSnpMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:172: missing file link 'ScanVcfParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFileList'
    pack-methods                            html  
    reduceByFile-methods                    html  
    reduceByRange-methods                   html  
    reduceByYield                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:12: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:29: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:121: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:122: missing file link 'TabixFile'
    registry-utils                          html  
    unpack-methods                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicFiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFiles' as GenomicFiles_1.14.0.zip
* DONE (GenomicFiles)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GenomicFiles.Rcheck/tests_i386/GenomicFiles_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("GenomicFiles")

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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Welcome to Bioconductor

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


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply


Attaching package: 'Biostrings'

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

    type

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

    strsplit

Warning messages:
Warning messages:
1: 1: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) :2:  '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) :3:  '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) :4:  '+' not meaningful for factors
In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
Warning messages:
1: 1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) : '+' not meaningful for factors


RUNIT TEST PROTOCOL -- Thu Apr 12 00:32:49 2018 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFiles RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence 19.
  Note that only ranges located on a non-circular sequence whose length
  is not NA can be 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.
> 
> proc.time()
   user  system elapsed 
  39.20    0.84  179.46 

GenomicFiles.Rcheck/tests_x64/GenomicFiles_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("GenomicFiles")

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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Welcome to Bioconductor

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


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply


Attaching package: 'Biostrings'

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

    type

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

    strsplit

Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
3: 1: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) :In Ops.factor(left, right) : '+' not meaningful for factors
 '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: 1: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors


RUNIT TEST PROTOCOL -- Thu Apr 12 00:36:14 2018 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFiles RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence 19.
  Note that only ranges located on a non-circular sequence whose length
  is not NA can be 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.
> 
> proc.time()
   user  system elapsed 
  42.07    0.62  204.07 

Example timings

GenomicFiles.Rcheck/examples_i386/GenomicFiles-Ex.timings

nameusersystemelapsed
GenomicFiles-class 0.83 0.0633.27
VcfStack-class 4.44 0.0231.92
pack-methods1.080.001.08
reduceByFile-methods 0.21 0.0064.36
reduceByRange-methods 0.22 0.0144.89
reduceByYield 1.24 0.0736.03
registry-utils000
unpack-methods1.110.001.11

GenomicFiles.Rcheck/examples_x64/GenomicFiles-Ex.timings

nameusersystemelapsed
GenomicFiles-class 1.61 0.0332.94
VcfStack-class 4.78 0.0432.29
pack-methods1.140.001.14
reduceByFile-methods 0.30 0.0065.09
reduceByRange-methods 0.28 0.0255.82
reduceByYield 1.84 0.0825.09
registry-utils000
unpack-methods0.770.050.82