BioC 3.6: CHECK report for AllelicImbalance on veracruz1

Package: AllelicImbalance

Version: 1.15.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.15.3.tar.gz

StartedAt: 2017-08-15 23:48:34 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:55:37 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 422.8 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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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_1.15.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.15.3’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 18.894  1.287  20.696
import-bam           13.238  0.262  13.892
lva                   6.302  0.016   6.509
annotation-wrappers   5.769  0.177   6.079
ASEset-glocationplot  5.728  0.067   5.924
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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: OK

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.442	0.008	0.465
ASEset-class	0.829	0.006	0.848
ASEset-filters	0.117	0.002	0.120
ASEset-gbarplot	0.033	0.002	0.035
ASEset-glocationplot	5.728	0.067	5.924
ASEset-gviztrack	0.838	0.011	0.874
ASEset-scanForHeterozygotes	2.223	0.016	2.309
ASEset.old	0.001	0.001	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.002	0.002	0.004
DetectedAI-class	0.068	0.002	0.071
DetectedAI-plot	2.040	0.009	2.115
DetectedAI-summary	0.070	0.004	0.074
GRvariants	0.002	0.001	0.003
GlobalAnalysis-class	0.003	0.001	0.004
LinkVariantAlmlof-class	0.001	0.000	0.000
LinkVariantAlmlof-plot	1.748	0.005	1.802
RegionSummary-class	0.001	0.000	0.001
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	5.769	0.177	6.079
annotationBarplot	0	0	0
barplot-lattice-support	0.744	0.006	0.778
binom.test	0.029	0.002	0.033
chisq.test	0.088	0.001	0.092
cigar-utilities	0.01	0.00	0.01
countAllelesFromBam	0.003	0.001	0.004
coverageMatrixListFromGAL	0.954	0.009	0.985
decorateWithExons	0.002	0.001	0.003
decorateWithGenes	0.002	0.002	0.003
defaultMapBias	0.046	0.002	0.049
defaultPhase	0.001	0.000	0.002
detectAI	0.055	0.002	0.057
fractionPlotDf	0.023	0.002	0.024
gba	0.000	0.000	0.001
genomatrix	0.000	0.000	0.001
genotype2phase	0.036	0.003	0.038
getAlleleCounts	4.434	0.016	4.553
getAlleleQuality	4.874	0.009	4.929
getAreaFromGeneNames	0.307	0.004	0.327
getDefaultMapBiasExpMean	0.024	0.002	0.025
getSnpIdFromLocation	18.894	1.287	20.696
histplot	0.001	0.000	0.000
implodeList-old	0.005	0.000	0.005
import-bam-2	0.008	0.000	0.009
import-bam	13.238	0.262	13.892
import-bcf	0.590	0.016	0.622
inferAlleles	0.068	0.001	0.072
inferAltAllele	0.013	0.001	0.013
inferGenotypes	0.062	0.002	0.064
initialize-ASEset	0.197	0.001	0.209
initialize-DetectedAI	0.040	0.001	0.041
initialize-GlobalAnalysis	0.005	0.000	0.006
initialize-RiskVariant	0.002	0.001	0.003
legendBarplot	0.001	0.000	0.001
locationplot	1.314	0.017	1.367
lva	6.302	0.016	6.509
lva.internal	0.235	0.002	0.245
makeMaskedFasta	0.655	0.003	0.685
mapBiasRef	0.008	0.001	0.009
minCountFilt	0.039	0.001	0.040
minFreqFilt	0.029	0.001	0.034
multiAllelicFilt	0.011	0.001	0.013
phase2genotype	0.017	0.003	0.020
phaseArray2phaseMatrix	0.008	0.002	0.010
phaseMatrix2Array	0.008	0.002	0.009
randomRef	0.015	0.001	0.016
reads	0.001	0.000	0.000
refAllele	0.015	0.001	0.016
regionSummary	0.442	0.002	0.454
scanForHeterozygotes-old	4.094	0.016	4.193