BioC 3.1: CHECK report for AllelicImbalance on moscato2

Package: AllelicImbalance

Version: 1.6.2

Command: rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.6.2.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.6.2.tar.gz

StartedAt: 2015-10-08 23:15:49 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:24:49 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 540.4 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.6.2.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.6.2.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/AllelicImbalance.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'AllelicImbalance' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [84s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     22.36   0.31   27.67
scanForHeterozygotes-old 10.05   0.03   10.08
import-bam                8.95   0.02    8.97
getAlleleCounts           5.73   0.00    5.73
annotation-wrappers       2.37   0.03    8.92
** running examples for arch 'x64' ... [84s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     20.78   0.30   21.08
scanForHeterozygotes-old 13.24   0.00   13.24
import-bam               12.78   0.01   12.79
getAlleleCounts           8.41   0.02    8.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [11s]
 [11s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [15s]
 [15s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/AllelicImbalance.Rcheck/00check.log'
for details.

install for i386

* 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'

install for x64

* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.6.2.zip
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.18	0.00	0.19
ASEset-class	0.07	0.00	0.06
ASEset-gbarplot	0.17	0.01	0.19
ASEset-glocationplot	2.43	0.05	2.48
ASEset-gviztrack	0.64	0.00	0.64
ASEset-scanForHeterozygotes	2.89	0.00	2.89
ASEset.sim	0	0	0
ASEsetFromBam	0	0	0
DetectedAI-class	0.09	0.00	0.09
GRvariants	0	0	0
GlobalAnalysis-class	0	0	0
ReferenceBias-class	0.08	0.00	0.08
ReferenceBias-show	0	0	0
annotation-wrappers	2.37	0.03	8.92
annotationBarplot	0	0	0
barplot-lattice-support	0.16	0.00	0.15
binom.test	0.05	0.00	0.05
boxplot	0.01	0.00	0.02
chisq.test	0.03	0.00	0.03
cigar-utilities	0.04	0.00	0.03
countAllelesFromBam	0.01	0.00	0.01
coverageMatrixListFromGAL	0.95	0.00	0.96
decorateWithExons	0	0	0
decorateWithGenes	0	0	0
defaultMapBias	0.03	0.00	0.03
defaultPhase	0.02	0.00	0.02
detectAI	0.04	0.00	0.04
fractionPlotDf	0.05	0.00	0.05
gba	0	0	0
genofilters	0.03	0.00	0.03
getAlleleCounts	5.73	0.00	5.73
getAreaFromGeneNames	0.62	0.00	0.62
getDefaultMapBiasExpMean	0.01	0.00	0.02
getSnpIdFromLocation	22.36	0.31	27.67
histplot	0	0	0
implodeList-old	0	0	0
import-bam-2	0.02	0.00	0.02
import-bam	8.95	0.02	8.97
import-bcf	0.39	0.00	0.40
inferAlleles	0	0	0
inferAltAllele	0.02	0.00	0.02
inferGenotypes	0.01	0.01	0.03
initialize-ASEset	0.02	0.00	0.02
initialize-DetectedAI	0.06	0.00	0.06
initialize-GlobalAnalysis	0.00	0.02	0.01
initialize-ReferenceBias	0.06	0.00	0.07
legendBarplot	0	0	0
locationplot	0.67	0.00	0.67
makeMaskedFasta	0.39	0.00	1.00
mapBiasRef	0.02	0.00	0.01
phaseArray2Matrix	0.01	0.00	0.02
phaseMatrix2Array	0.02	0.00	0.01
randomRef	0.03	0.00	0.03
reads	0	0	0
refAllele	0.02	0.00	0.02
refFraction	0.01	0.02	0.03
regionSummary	0.14	0.00	0.14
scanForHeterozygotes-old	10.05	0.03	10.08

name	user	system	elapsed
ASEset-barplot	0.14	0.00	0.14
ASEset-class	0.08	0.00	0.07
ASEset-gbarplot	0.11	0.02	0.13
ASEset-glocationplot	2.57	0.01	2.59
ASEset-gviztrack	0.55	0.02	0.56
ASEset-scanForHeterozygotes	3.10	0.02	3.12
ASEset.sim	0	0	0
ASEsetFromBam	0.00	0.01	0.02
DetectedAI-class	0.06	0.00	0.06
GRvariants	0	0	0
GlobalAnalysis-class	0.02	0.00	0.01
ReferenceBias-class	0.06	0.00	0.07
ReferenceBias-show	0	0	0
annotation-wrappers	2.95	0.06	4.19
annotationBarplot	0	0	0
barplot-lattice-support	0.19	0.02	0.20
binom.test	0.05	0.00	0.04
boxplot	0.05	0.00	0.05
chisq.test	0.04	0.00	0.05
cigar-utilities	0.03	0.00	0.03
countAllelesFromBam	0	0	0
coverageMatrixListFromGAL	1.38	0.01	1.39
decorateWithExons	0	0	0
decorateWithGenes	0	0	0
defaultMapBias	0.04	0.00	0.04
defaultPhase	0	0	0
detectAI	0.08	0.00	0.08
fractionPlotDf	0.05	0.00	0.05
gba	0	0	0
genofilters	0.03	0.00	0.03
getAlleleCounts	8.41	0.02	8.42
getAreaFromGeneNames	0.65	0.01	0.67
getDefaultMapBiasExpMean	0	0	0
getSnpIdFromLocation	20.78	0.30	21.08
histplot	0	0	0
implodeList-old	0.01	0.00	0.01
import-bam-2	0	0	0
import-bam	12.78	0.01	12.79
import-bcf	0.50	0.02	0.53
inferAlleles	0	0	0
inferAltAllele	0.01	0.00	0.02
inferGenotypes	0.04	0.00	0.03
initialize-ASEset	0.03	0.00	0.03
initialize-DetectedAI	0.06	0.00	0.06
initialize-GlobalAnalysis	0.00	0.02	0.02
initialize-ReferenceBias	0.08	0.00	0.08
legendBarplot	0	0	0
locationplot	0.56	0.04	0.61
makeMaskedFasta	0.48	0.00	0.50
mapBiasRef	0	0	0
phaseArray2Matrix	0	0	0
phaseMatrix2Array	0.01	0.00	0.01
randomRef	0.03	0.00	0.03
reads	0	0	0
refAllele	0.02	0.00	0.02
refFraction	0.03	0.00	0.03
regionSummary	0.13	0.00	0.13
scanForHeterozygotes-old	13.24	0.00	13.24