Package: AllelicImbalance

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.18.0.tar.gz

StartedAt: 2018-10-16 19:49:40 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 19:57:16 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 455.3 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 --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.18.0’
* 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 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 ... NOTE
  Failed with error:  'package 'DelayedArray' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'AllelicImbalance'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 23.038  1.646  24.830
annotation-wrappers  20.175  0.326  20.645
import-bam           18.546  0.411  19.088
lva                   9.901  0.024   9.981
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AllelicImbalance
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("AllelicImbalance")
Loading required package: AllelicImbalance
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 96 SKIPPED: 1 FAILED: 0
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.378   0.796  18.299 

name	user	system	elapsed
ASEset-barplot	0.451	0.054	0.509
ASEset-class	0.585	0.008	0.596
ASEset-filters	0.125	0.010	0.136
ASEset-gbarplot	0.106	0.017	0.124
ASEset-glocationplot	4.221	0.046	4.304
ASEset-gviztrack	0.578	0.008	0.591
ASEset-scanForHeterozygotes	2.219	0.015	2.250
ASEset.old	0.002	0.000	0.002
ASEset.sim	0.002	0.000	0.001
ASEsetFromBam	0.003	0.001	0.004
DetectedAI-class	0.195	0.002	0.198
DetectedAI-plot	1.977	0.010	2.012
DetectedAI-summary	0.218	0.005	0.224
GRvariants	0.002	0.002	0.004
GlobalAnalysis-class	0.002	0.001	0.004
LinkVariantAlmlof-class	0.001	0.000	0.001
LinkVariantAlmlof-plot	2.286	0.006	2.330
RegionSummary-class	0.002	0.001	0.002
RiskVariant-class	0.001	0.000	0.001
annotation-wrappers	20.175	0.326	20.645
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.239	0.002	0.245
binom.test	0.122	0.003	0.125
chisq.test	0.288	0.006	0.295
cigar-utilities	0.015	0.000	0.016
countAllelesFromBam	0.004	0.002	0.006
coverageMatrixListFromGAL	1.024	0.068	1.101
decorateWithExons	0.003	0.002	0.007
decorateWithGenes	0.002	0.001	0.004
defaultMapBias	0.038	0.006	0.046
defaultPhase	0.003	0.000	0.004
detectAI	0.228	0.033	0.269
fractionPlotDf	0.062	0.011	0.075
gba	0.001	0.000	0.001
genomatrix	0.001	0.000	0.001
genotype2phase	0.087	0.004	0.092
getAlleleCounts	4.807	0.021	4.867
getAlleleQuality	4.723	0.016	4.773
getAreaFromGeneNames	0.322	0.007	0.330
getDefaultMapBiasExpMean	0.057	0.003	0.060
getSnpIdFromLocation	23.038	1.646	24.830
histplot	0.001	0.000	0.001
implodeList-old	0.007	0.000	0.007
import-bam-2	0.012	0.001	0.012
import-bam	18.546	0.411	19.088
import-bcf	0.849	0.025	0.879
inferAlleles	0.029	0.001	0.031
inferAltAllele	0.041	0.002	0.042
inferGenotypes	0.069	0.002	0.071
initialize-ASEset	0.075	0.001	0.076
initialize-DetectedAI	0.173	0.002	0.177
initialize-GlobalAnalysis	0.006	0.003	0.009
initialize-RiskVariant	0.003	0.001	0.005
legendBarplot	0.001	0.000	0.002
locationplot	2.163	0.051	2.227
lva	9.901	0.024	9.981
lva.internal	0.384	0.003	0.390
makeMaskedFasta	0.867	0.026	0.899
mapBiasRef	0.022	0.003	0.024
minCountFilt	0.167	0.002	0.172
minFreqFilt	0.162	0.002	0.168
multiAllelicFilt	0.036	0.002	0.040
phase2genotype	0.043	0.002	0.045
phaseArray2phaseMatrix	0.010	0.002	0.013
phaseMatrix2Array	0.008	0.002	0.009
randomRef	0.041	0.002	0.043
reads	0.001	0.000	0.001
refAllele	0.019	0.003	0.021
regionSummary	0.613	0.017	0.629
scanForHeterozygotes-old	4.423	0.042	4.489