BioC 3.1: CHECK report for AllelicImbalance on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.6.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [19s/19s] 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 ... [65s/66s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     19.291  0.079  19.448
scanForHeterozygotes-old 10.411  0.024  10.436
import-bam                9.370  0.008   9.431
getAlleleCounts           5.554  0.000   5.550
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [10s/10s]
 [10s/10s] 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
  ‘/home/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	0.116	0.004	0.120
ASEset-class	0.071	0.000	0.071
ASEset-gbarplot	0.105	0.000	0.105
ASEset-glocationplot	2.010	0.008	2.019
ASEset-gviztrack	0.421	0.004	0.424
ASEset-scanForHeterozygotes	2.666	0.004	2.668
ASEset.sim	0	0	0
ASEsetFromBam	0.002	0.000	0.002
DetectedAI-class	0.054	0.004	0.058
GRvariants	0.001	0.000	0.001
GlobalAnalysis-class	0.002	0.000	0.002
ReferenceBias-class	0.06	0.00	0.06
ReferenceBias-show	0.001	0.000	0.001
annotation-wrappers	2.129	0.028	2.155
annotationBarplot	0.001	0.000	0.000
barplot-lattice-support	0.141	0.016	0.157
binom.test	0.044	0.000	0.044
boxplot	0.026	0.000	0.026
chisq.test	0.032	0.000	0.032
cigar-utilities	0.02	0.00	0.02
countAllelesFromBam	0.002	0.000	0.002
coverageMatrixListFromGAL	1.016	0.004	1.019
decorateWithExons	0.002	0.000	0.002
decorateWithGenes	0.001	0.000	0.002
defaultMapBias	0.032	0.000	0.031
defaultPhase	0.000	0.000	0.001
detectAI	0.057	0.000	0.059
fractionPlotDf	0.037	0.000	0.037
gba	0.001	0.000	0.000
genofilters	0.026	0.001	0.026
getAlleleCounts	5.554	0.000	5.550
getAreaFromGeneNames	0.354	0.004	0.358
getDefaultMapBiasExpMean	0.008	0.000	0.008
getSnpIdFromLocation	19.291	0.079	19.448
histplot	0.000	0.000	0.001
implodeList-old	0.001	0.000	0.001
import-bam-2	0.007	0.000	0.007
import-bam	9.370	0.008	9.431
import-bcf	0.443	0.008	0.451
inferAlleles	0.007	0.000	0.007
inferAltAllele	0.011	0.000	0.011
inferGenotypes	0.018	0.000	0.018
initialize-ASEset	0.023	0.000	0.023
initialize-DetectedAI	0.056	0.000	0.056
initialize-GlobalAnalysis	0.004	0.000	0.005
initialize-ReferenceBias	0.059	0.000	0.059
legendBarplot	0.001	0.000	0.000
locationplot	0.49	0.00	0.49
makeMaskedFasta	0.431	0.008	0.440
mapBiasRef	0.011	0.000	0.011
phaseArray2Matrix	0.009	0.000	0.009
phaseMatrix2Array	0.008	0.000	0.008
randomRef	0.025	0.000	0.024
reads	0.000	0.000	0.001
refAllele	0.014	0.000	0.014
refFraction	0.021	0.000	0.020
regionSummary	0.103	0.000	0.104
scanForHeterozygotes-old	10.411	0.024	10.436

BioC 3.1: CHECK report for AllelicImbalance on zin2

Summary

Command output