BioC 3.5: CHECK report for AllelicImbalance on malbec2

Package: AllelicImbalance

Version: 1.14.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz

StartedAt: 2017-08-15 21:04:33 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:11:03 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 390.3 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.14.0’
* 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 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 17.760  6.044  27.476
import-bam           15.380  0.116  15.515
annotation-wrappers   6.168  0.132   8.337
* 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	0.340	0.004	0.343
ASEset-class	0.564	0.000	0.564
ASEset-filters	0.084	0.000	0.085
ASEset-gbarplot	0.028	0.000	0.028
ASEset-glocationplot	4.504	0.016	4.525
ASEset-gviztrack	0.676	0.000	0.677
ASEset-scanForHeterozygotes	2.708	0.040	2.749
ASEset.old	0.000	0.000	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.000	0.000	0.002
DetectedAI-class	0.048	0.000	0.048
DetectedAI-plot	1.428	0.000	1.430
DetectedAI-summary	0.056	0.004	0.062
GRvariants	0.004	0.000	0.002
GlobalAnalysis-class	0.000	0.000	0.002
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	1.280	0.000	1.282
RegionSummary-class	0	0	0
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	6.168	0.132	8.337
annotationBarplot	0	0	0
barplot-lattice-support	0.124	0.000	0.124
binom.test	0.024	0.004	0.026
chisq.test	0.076	0.000	0.076
cigar-utilities	0.012	0.000	0.011
countAllelesFromBam	0.000	0.004	0.002
coverageMatrixListFromGAL	0.776	0.000	0.777
decorateWithExons	0.000	0.000	0.002
decorateWithGenes	0.004	0.000	0.002
defaultMapBias	0.068	0.000	0.067
defaultPhase	0.000	0.000	0.002
detectAI	0.044	0.000	0.044
fractionPlotDf	0.024	0.000	0.024
gba	0	0	0
genomatrix	0.000	0.000	0.001
genotype2phase	0.028	0.000	0.028
getAlleleCounts	4.524	0.000	4.526
getAlleleQuality	3.876	0.000	3.881
getAreaFromGeneNames	0.284	0.000	0.284
getDefaultMapBiasExpMean	0.02	0.00	0.02
getSnpIdFromLocation	17.760	6.044	27.476
histplot	0	0	0
implodeList-old	0.004	0.000	0.006
import-bam-2	0.004	0.000	0.006
import-bam	15.380	0.116	15.515
import-bcf	0.720	0.044	0.765
inferAlleles	0.064	0.000	0.063
inferAltAllele	0.012	0.000	0.012
inferGenotypes	0.060	0.000	0.063
initialize-ASEset	0.164	0.000	0.164
initialize-DetectedAI	0.036	0.004	0.043
initialize-GlobalAnalysis	0.004	0.000	0.004
initialize-RiskVariant	0.004	0.000	0.002
legendBarplot	0	0	0
locationplot	1.276	0.004	1.283
lva	3.892	0.008	3.907
lva.internal	0.168	0.004	0.175
makeMaskedFasta	0.708	0.000	0.710
mapBiasRef	0.008	0.000	0.010
minCountFilt	0.028	0.000	0.026
minFreqFilt	0.024	0.000	0.025
multiAllelicFilt	0.008	0.000	0.009
phase2genotype	0.016	0.000	0.015
phaseArray2phaseMatrix	0.008	0.000	0.007
phaseMatrix2Array	0.008	0.000	0.006
randomRef	0.012	0.000	0.012
reads	0	0	0
refAllele	0.012	0.000	0.012
regionSummary	0.352	0.000	0.351
scanForHeterozygotes-old	4.032	0.000	4.043