VariantTools 1.4.5
Michael Lawrence
| Snapshot Date: 2014-02-27 16:20:29 -0800 (Thu, 27 Feb 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/VariantTools | | Last Changed Rev: 83235 / Revision: 86906 | | Last Changed Date: 2013-11-12 16:23:33 -0800 (Tue, 12 Nov 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | N O T S U P P O R T E D |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/VariantTools.Rcheck’
* using R version 3.0.2 Patched (2013-12-18 r64488)
* 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 ‘1.4.5’
* 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 ... [25s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘IRanges’ ‘GenomicRanges’ ‘VariantAnnotation’ ‘methods’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... WARNING
‘::’ or ‘:::’ import not declared from: ‘graph’
Unexported objects imported by ‘:::’ calls:
‘BiocGenerics:::testPackage’ ‘IRanges:::asList’ ‘IRanges:::mseq’
‘gmapR:::normalizeIndelAlleles’ ‘gmapR:::showSlots’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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’
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’
makeVRangesFromVariantGRanges: no visible binding for global variable
‘high.quality.total’
makeVRangesFromVariantGRanges: no visible binding for global variable
‘high.quality.ref’
makeVRangesFromVariantGRanges: no visible binding for global variable
‘high.quality’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'callSampleSpecificVariants':
\S4method{callSampleSpecificVariants}{BamFile,BamFile}
Code: function(case, control, tally.param, calling.filters =
VariantCallingFilters(), post.filters = FilterRules(),
...)
Docs: function(case, control, tally.param, ...)
Argument names in code not in docs:
calling.filters post.filters
Mismatches in argument names:
Position: 4 Code: calling.filters Docs: ...
* 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 ... [46s/46s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
postFilterVariants 10.569 0.556 11.259
callWildtype 9.468 0.420 10.069
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘VariantTools_unit_tests.R’ [0s/0s]
[0s/0s] 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
WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/VariantTools.Rcheck/00check.log’
for details.