BioC 3.1: CHECK report for AllelicImbalance on morelia

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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 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [24s/24s] 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’
CoverageDataTrack,ASEset: no visible global function definition for
  ‘DataTrack’
countAllelesFromBam,GRanges : .local: no visible binding for global
  variable ‘UserDir’
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 ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     19.633  1.010  20.859
scanForHeterozygotes-old 12.224  0.371  12.665
import-bam                9.299  0.608  10.025
getAlleleCounts           6.258  0.275   6.534
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [12s/12s]
 [13s/13s] 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	0.149	0.003	0.152
ASEset-class	0.069	0.000	0.070
ASEset-gbarplot	0.138	0.001	0.139
ASEset-glocationplot	2.275	0.088	2.365
ASEset-gviztrack	0.402	0.010	0.412
ASEset-scanForHeterozygotes	2.796	0.125	2.921
ASEset.sim	0	0	0
ASEsetFromBam	0.002	0.000	0.002
DetectedAI-class	0.056	0.000	0.057
GRvariants	0.001	0.001	0.001
GlobalAnalysis-class	0.001	0.000	0.002
ReferenceBias-class	0.05	0.00	0.05
ReferenceBias-show	0.001	0.000	0.001
annotation-wrappers	2.412	0.275	2.714
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.201	0.032	0.233
binom.test	0.057	0.009	0.067
boxplot	0.030	0.001	0.031
chisq.test	0.045	0.002	0.046
cigar-utilities	0.031	0.007	0.038
countAllelesFromBam	0.002	0.002	0.003
coverageMatrixListFromGAL	1.184	0.096	1.279
decorateWithExons	0.002	0.000	0.002
decorateWithGenes	0.002	0.001	0.002
defaultMapBias	0.033	0.009	0.041
defaultPhase	0.000	0.001	0.001
detectAI	0.055	0.016	0.071
fractionPlotDf	0.040	0.009	0.049
gba	0.001	0.001	0.001
genofilters	0.025	0.008	0.033
getAlleleCounts	6.258	0.275	6.534
getAreaFromGeneNames	0.386	0.008	0.394
getDefaultMapBiasExpMean	0.010	0.000	0.011
getSnpIdFromLocation	19.633	1.010	20.859
histplot	0.000	0.000	0.001
implodeList-old	0.002	0.000	0.002
import-bam-2	0.01	0.00	0.01
import-bam	9.299	0.608	10.025
import-bcf	0.465	0.062	0.539
inferAlleles	0.008	0.000	0.009
inferAltAllele	0.012	0.000	0.013
inferGenotypes	0.024	0.000	0.025
initialize-ASEset	0.032	0.005	0.037
initialize-DetectedAI	0.077	0.001	0.077
initialize-GlobalAnalysis	0.006	0.000	0.005
initialize-ReferenceBias	0.069	0.001	0.070
legendBarplot	0	0	0
locationplot	0.645	0.033	0.680
makeMaskedFasta	0.416	0.024	0.441
mapBiasRef	0.009	0.000	0.009
phaseArray2Matrix	0.013	0.000	0.013
phaseMatrix2Array	0.011	0.001	0.012
randomRef	0.029	0.000	0.029
reads	0.001	0.001	0.000
refAllele	0.015	0.000	0.015
refFraction	0.025	0.001	0.026
regionSummary	0.126	0.002	0.128
scanForHeterozygotes-old	12.224	0.371	12.665

BioC 3.1: CHECK report for AllelicImbalance on morelia

Summary

Command output