BioC 2.12: CHECK report for VariantTools on george2

Package: VariantTools

Version: 1.1.13

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.1.13.tar.gz

StartedAt: 2013-03-25 05:03:39 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:14:15 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 636.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: VariantTools.Rcheck

Warnings: 3

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/VariantTools.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantTools’ version ‘1.1.13’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VariantTools’ can be installed ... [55s/58s] OK
* checking installed package size ... OK
* checking package 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
* 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 for unstated 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 ... NOTE
BinomialLRFilter : <anonymous>: no visible binding for global variable
  ‘high.quality’
BinomialLRFilter : <anonymous>: no visible binding for global variable
  ‘high.quality.total’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.pos.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.neg.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.pos’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.neg’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘high.quality’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘high.quality.total’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.mean’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.mean.ref’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.var’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.var.ref’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘count’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘count.ref’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘VariantPostFilters’ ‘calculateConcordanceMatrix’
  ‘calculateConcordanceReport’ ‘callWildtype’ ‘idVerify’
  ‘matchVariants’ ‘mergeVariantInfo’ ‘minCallableCoverage’
  ‘printConcordanceReport’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'callSampleSpecificVariants':
\S4method{callSampleSpecificVariants}{GenomicRanges,GenomicRanges}
  Code: function(case, control, control.cov, qa.filters =
                 VariantQAFilters(), calling.filters =
                 VariantCallingFilters(), post.filters =
                 VariantPostFilters(), ...)
  Docs: function(case, control, control.cov, qa.filters =
                 VariantQAFilters(), calling.filters =
                 VariantCallingFilters(), ...)
  Argument names in code not in docs:
    post.filters
  Mismatches in argument names:
    Position: 6 Code: post.filters Docs: ...

Codoc mismatches from documentation object 'callVariants':
\S4method{callVariants}{GenomicRanges}
  Code: function(x, calling.filters = VariantCallingFilters(...),
                 post.filters = VariantPostFilters(), ...)
  Docs: function(x, calling.filters = VariantCallingFilters(...), ...)
  Argument names in code not in docs:
    post.filters
  Mismatches in argument names:
    Position: 3 Code: post.filters Docs: ...
VariantCallingFilters
  Code: function(read.count = 2L, p.lower = 0.2, p.error = 1/1000)
  Docs: function(read.count = 2L, p.lower = 0.2, p.error = 1e-04)
  Mismatches in argument default values:
    Name: 'p.error' Code: 1/1000 Docs: 1e-04
VariantPostFilters
  Code: function(max.nbor.count = 0.1, whitelist = NULL)
  Docs: function(max.nbor.count = 0.1)
  Argument names in code not in docs:
    whitelist

Codoc mismatches from documentation object 'qaVariants':
VariantQAFilters
  Code: function(cycle.count = 2L, fisher.strand.p.value = 1e-04,
                 read.pos.p.value = 1e-04, mask = GRanges())
  Docs: function(cycle.count = 2L, fisher.strand.p.value = 0.001, mask
                 = GRanges())
  Argument names in code not in docs:
    read.pos.p.value
  Mismatches in argument names:
    Position: 3 Code: read.pos.p.value Docs: mask
  Mismatches in argument default values:
    Name: 'fisher.strand.p.value' Code: 1e-04 Docs: 0.001

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'callVariants':
  ‘VariantPostFilters’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [174s/144s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
callSampleSpecificVariants 60.919  1.944  71.030
callVariants               40.215  2.292  16.064
variantGR2Vcf              19.525  2.600  15.782
tallyVariants              12.521  1.852   6.749
qaVariants                  5.408  0.708   7.159
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantTools_unit_tests.R’ [0s/0s]
 [1s/1s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/VariantTools.Rcheck/00check.log’
for details.

* installing *source* package ‘VariantTools’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘VariantTools.Rnw’ 
** testing if installed package can be loaded
* DONE (VariantTools)

name	user	system	elapsed
callSampleSpecificVariants	60.919	1.944	71.030
callVariants	40.215	2.292	16.064
qaVariants	5.408	0.708	7.159
tallyVariants	12.521	1.852	6.749
variantGR2Vcf	19.525	2.600	15.782

Summary

Command output