BioC 3.5: CHECK report for AllelicImbalance on oaxaca

Package: AllelicImbalance

Version: 1.13.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.13.2.tar.gz

StartedAt: 2017-03-03 22:57:09 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:05:02 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 472.6 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_1.13.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.13.2’
* 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     20.002  1.288  28.378
import-bam               13.854  0.389  14.251
annotation-wrappers       7.777  0.496  10.657
scanForHeterozygotes-old  5.355  0.015   5.380
getAlleleCounts           5.200  0.013   5.215
* 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	0.525	0.024	0.548
ASEset-class	0.844	0.008	0.853
ASEset-filters	0.077	0.001	0.078
ASEset-gbarplot	0.025	0.001	0.026
ASEset-glocationplot	4.874	0.016	4.893
ASEset-gviztrack	0.863	0.009	0.871
ASEset-scanForHeterozygotes	2.842	0.047	2.890
ASEset.old	0	0	0
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.003	0.002	0.005
DetectedAI-class	0.078	0.002	0.079
DetectedAI-plot	2.162	0.012	2.278
DetectedAI-summary	0.060	0.004	0.064
GRvariants	0.002	0.001	0.002
GlobalAnalysis-class	0.001	0.001	0.002
LinkVariantAlmlof-class	0.001	0.000	0.000
LinkVariantAlmlof-plot	1.528	0.005	1.533
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	7.777	0.496	10.657
annotationBarplot	0.001	0.000	0.000
barplot-lattice-support	0.166	0.001	0.167
binom.test	0.030	0.002	0.031
chisq.test	0.129	0.002	0.131
cigar-utilities	0.018	0.001	0.018
countAllelesFromBam	0.003	0.001	0.004
coverageMatrixListFromGAL	0.972	0.009	0.980
decorateWithExons	0.002	0.002	0.004
decorateWithGenes	0.001	0.001	0.003
defaultMapBias	0.049	0.002	0.051
defaultPhase	0.001	0.001	0.001
detectAI	0.068	0.002	0.071
fractionPlotDf	0.033	0.002	0.034
gba	0.000	0.000	0.001
genomatrix	0	0	0
genotype2phase	0.034	0.003	0.037
getAlleleCounts	5.200	0.013	5.215
getAlleleQuality	4.947	0.009	4.957
getAreaFromGeneNames	0.343	0.005	0.348
getDefaultMapBiasExpMean	0.031	0.001	0.031
getSnpIdFromLocation	20.002	1.288	28.378
histplot	0.000	0.000	0.001
implodeList-old	0.01	0.00	0.01
import-bam-2	0.010	0.001	0.010
import-bam	13.854	0.389	14.251
import-bcf	0.672	0.028	0.699
inferAlleles	0.103	0.001	0.104
inferAltAllele	0.016	0.001	0.016
inferGenotypes	0.075	0.001	0.076
initialize-ASEset	0.169	0.000	0.170
initialize-DetectedAI	0.042	0.001	0.042
initialize-GlobalAnalysis	0.005	0.001	0.006
initialize-RiskVariant	0.002	0.001	0.002
legendBarplot	0.001	0.000	0.000
locationplot	2.014	0.024	2.048
lva	4.726	0.020	4.819
lva.internal	0.271	0.002	0.273
makeMaskedFasta	0.586	0.003	0.590
mapBiasRef	0.008	0.001	0.009
minCountFilt	0.026	0.001	0.027
minFreqFilt	0.035	0.001	0.035
multiAllelicFilt	0.008	0.001	0.009
phase2genotype	0.027	0.003	0.030
phaseArray2phaseMatrix	0.009	0.002	0.010
phaseMatrix2Array	0.008	0.001	0.009
randomRef	0.010	0.001	0.011
reads	0	0	0
refAllele	0.013	0.001	0.014
regionSummary	0.474	0.003	0.478
scanForHeterozygotes-old	5.355	0.015	5.380