BioC 3.5: CHECK report for AllelicImbalance on veracruz2

Package: AllelicImbalance

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz

StartedAt: 2017-10-18 00:18:32 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:26:01 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 449.3 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.14.0’
* 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 21.663  1.477  23.835
import-bam           15.028  0.384  15.878
annotation-wrappers   7.020  0.234   7.478
ASEset-glocationplot  5.368  0.037   5.572
getAlleleCounts       5.292  0.031   5.471
getAlleleQuality      5.227  0.028   5.405
* 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	0.465	0.019	0.495
ASEset-class	0.861	0.008	0.907
ASEset-filters	0.111	0.002	0.115
ASEset-gbarplot	0.039	0.003	0.043
ASEset-glocationplot	5.368	0.037	5.572
ASEset-gviztrack	0.907	0.012	0.945
ASEset-scanForHeterozygotes	3.233	0.078	3.414
ASEset.old	0.001	0.000	0.001
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.002	0.001	0.003
DetectedAI-class	0.063	0.002	0.066
DetectedAI-plot	2.049	0.019	2.121
DetectedAI-summary	0.086	0.005	0.092
GRvariants	0.002	0.002	0.003
GlobalAnalysis-class	0.002	0.001	0.003
LinkVariantAlmlof-class	0.001	0.000	0.000
LinkVariantAlmlof-plot	1.726	0.010	1.799
RegionSummary-class	0.001	0.000	0.001
RiskVariant-class	0.001	0.000	0.000
annotation-wrappers	7.020	0.234	7.478
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.160	0.001	0.180
binom.test	0.026	0.001	0.027
chisq.test	0.090	0.002	0.095
cigar-utilities	0.013	0.000	0.013
countAllelesFromBam	0.002	0.001	0.003
coverageMatrixListFromGAL	1.046	0.007	1.093
decorateWithExons	0.002	0.001	0.003
decorateWithGenes	0.003	0.001	0.003
defaultMapBias	0.082	0.003	0.087
defaultPhase	0.002	0.000	0.002
detectAI	0.052	0.002	0.056
fractionPlotDf	0.029	0.001	0.030
gba	0.001	0.000	0.001
genomatrix	0.001	0.000	0.001
genotype2phase	0.037	0.003	0.040
getAlleleCounts	5.292	0.031	5.471
getAlleleQuality	5.227	0.028	5.405
getAreaFromGeneNames	0.318	0.007	0.335
getDefaultMapBiasExpMean	0.027	0.001	0.030
getSnpIdFromLocation	21.663	1.477	23.835
histplot	0.001	0.000	0.001
implodeList-old	0.008	0.000	0.009
import-bam-2	0.009	0.000	0.010
import-bam	15.028	0.384	15.878
import-bcf	0.669	0.023	0.729
inferAlleles	0.086	0.002	0.094
inferAltAllele	0.013	0.001	0.014
inferGenotypes	0.080	0.002	0.083
initialize-ASEset	0.192	0.001	0.195
initialize-DetectedAI	0.048	0.002	0.050
initialize-GlobalAnalysis	0.005	0.001	0.006
initialize-RiskVariant	0.002	0.002	0.003
legendBarplot	0.000	0.000	0.001
locationplot	1.619	0.021	1.694
lva	4.631	0.026	4.819
lva.internal	0.257	0.003	0.291
makeMaskedFasta	0.697	0.004	0.744
mapBiasRef	0.011	0.001	0.013
minCountFilt	0.035	0.001	0.038
minFreqFilt	0.032	0.002	0.034
multiAllelicFilt	0.011	0.002	0.012
phase2genotype	0.019	0.003	0.022
phaseArray2phaseMatrix	0.009	0.002	0.010
phaseMatrix2Array	0.008	0.001	0.009
randomRef	0.014	0.002	0.015
reads	0.001	0.000	0.001
refAllele	0.016	0.002	0.018
regionSummary	0.425	0.003	0.437
scanForHeterozygotes-old	4.484	0.029	4.714