BioC 3.1: CHECK report for AllelicImbalance on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.6.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘AllelicImbalance’ can be installed ... [36s/37s] 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:
  ‘Gviz’ ‘VariantAnnotation’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Gviz’
  All declared Imports should be used.
Package in Depends field not imported from: ‘Gviz’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
barplotLatticeCounts: no visible binding for global variable ‘alleles’
barplotLatticeFraction: no visible binding for global variable ‘groups’
ASEDAnnotationTrack,ASEset: no visible global function definition for
  ‘AnnotationTrack’
countAllelesFromBam,GRanges : .local: no visible binding for global
  variable ‘UserDir’
CoverageDataTrack,ASEset: no visible global function definition for
  ‘DataTrack’
getSnpIdFromLocation,GRanges : .local: no visible global function
  definition for ‘getSNPlocs’
glocationplot,ASEset: no visible global function definition for
  ‘GeneRegionTrack’
glocationplot,ASEset: no visible global function definition for
  ‘plotTracks’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [111s/117s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     28.854  1.078  33.326
scanForHeterozygotes-old 17.905  0.059  17.976
import-bam               15.780  0.383  16.732
getAlleleCounts           9.893  0.047  10.057
annotation-wrappers       4.410  0.311   5.540
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [20s/20s]
 [20s/20s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** inst
** preparing package for lazy loading
Creating a generic function for ‘ref’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘ref<-’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘alt’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘alt<-’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘binom.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘chisq.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘AllelicImbalance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.179	0.007	0.186
ASEset-class	0.082	0.000	0.082
ASEset-gbarplot	0.183	0.001	0.194
ASEset-glocationplot	3.507	0.066	3.632
ASEset-gviztrack	0.726	0.007	0.733
ASEset-scanForHeterozygotes	4.071	0.014	4.086
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.003	0.001	0.004
DetectedAI-class	0.139	0.002	0.141
GRvariants	0.004	0.000	0.004
GlobalAnalysis-class	0.003	0.000	0.004
ReferenceBias-class	0.136	0.001	0.140
ReferenceBias-show	0.001	0.000	0.000
annotation-wrappers	4.410	0.311	5.540
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.313	0.013	0.326
binom.test	0.085	0.014	0.099
boxplot	0.033	0.006	0.038
chisq.test	0.081	0.002	0.082
cigar-utilities	0.038	0.000	0.038
countAllelesFromBam	0.003	0.000	0.003
coverageMatrixListFromGAL	2.441	0.039	2.481
decorateWithExons	0.003	0.000	0.003
decorateWithGenes	0.003	0.000	0.004
defaultMapBias	0.060	0.002	0.062
defaultPhase	0.002	0.001	0.003
detectAI	0.113	0.001	0.115
fractionPlotDf	0.068	0.001	0.068
gba	0.001	0.000	0.001
genofilters	0.043	0.001	0.044
getAlleleCounts	9.893	0.047	10.057
getAreaFromGeneNames	0.682	0.009	0.692
getDefaultMapBiasExpMean	0.013	0.001	0.013
getSnpIdFromLocation	28.854	1.078	33.326
histplot	0.001	0.001	0.001
implodeList-old	0.003	0.000	0.004
import-bam-2	0.012	0.001	0.012
import-bam	15.780	0.383	16.732
import-bcf	0.780	0.050	0.861
inferAlleles	0.010	0.001	0.010
inferAltAllele	0.021	0.001	0.022
inferGenotypes	0.032	0.001	0.032
initialize-ASEset	0.048	0.001	0.049
initialize-DetectedAI	0.114	0.001	0.115
initialize-GlobalAnalysis	0.007	0.001	0.007
initialize-ReferenceBias	0.099	0.001	0.099
legendBarplot	0.001	0.000	0.001
locationplot	0.965	0.013	1.130
makeMaskedFasta	0.729	0.014	0.744
mapBiasRef	0.020	0.001	0.021
phaseArray2Matrix	0.019	0.001	0.020
phaseMatrix2Array	0.020	0.001	0.021
randomRef	0.055	0.001	0.056
reads	0.001	0.000	0.001
refAllele	0.025	0.001	0.027
refFraction	0.047	0.001	0.048
regionSummary	0.200	0.001	0.200
scanForHeterozygotes-old	17.905	0.059	17.976

BioC 3.1: CHECK report for AllelicImbalance on petty

Summary

Command output