VariantTools 1.1.9
Michael Lawrence
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VariantTools | | Last Changed Rev: 72009 / Revision: 72575 | | Last Changed Date: 2012-12-17 14:49:44 -0800 (Mon, 17 Dec 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | N O T S U P P O R T E D |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/VariantTools.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.1.9’
* 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 ... 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’
BinomialLRFilter : <anonymous>: no visible binding for global variable
‘count’
BinomialLRFilter : <anonymous>: no visible binding for global variable
‘count.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’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘count’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable ‘count.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:
‘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 'callVariants':
VariantCallingFilters
Code: function(read.count = 2L, p.lower = 0.2, p.error = if
(use.high.qual) 1/10000 else 1/100, use.high.qual =
TRUE)
Docs: function(read.count = 2L, p.lower = 0.2, p.error = 1/1000,
use.high.qual = TRUE)
Mismatches in argument default values:
Name: 'p.error' Code: if (use.high.qual) 1/10000 else 1/100 Docs: 1/1000
Codoc mismatches from documentation object 'qaVariants':
VariantQAFilters
Code: function(cycle.count = 2L, fisher.strand.p.value = 1e-04,
read.pos.p.value = 1e-04)
Docs: function(cycle.count = 2L, fisher.strand.p.value = 0.001)
Argument names in code not in docs:
read.pos.p.value
Mismatches in argument default values:
Name: 'fisher.strand.p.value' Code: 1e-04 Docs: 0.001
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
callSampleSpecificVariants 34.990 1.140 39.101
callVariants 23.470 1.108 6.843
variantGR2Vcf 14.209 1.540 8.418
qaVariants 5.236 0.580 3.758
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘VariantTools_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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/VariantTools.Rcheck/00check.log’
for details.