Multiple platform build/check report for BioC 3.9 - CHECK report for AllelicImbalance on merida2

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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_1.21.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.21.2’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 21.861  1.516  23.467
import-bam           18.981  0.384  19.502
lva                   9.783  0.020   9.862
annotation-wrappers   6.326  0.571   7.719
ASEset-glocationplot  5.505  0.185   5.738
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 4. Failure: test store and access of phase (@test_phase.R#37)  ──────────────
  `x` not equal to `expected`.
  2/4 mismatches (average diff: 1)
  [1] 1 - 0 ==  1
  [2] 0 - 1 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 92 SKIPPED: 1 FAILED: 4
  1. Failure: test store and access of phase (@test_phase.R#31) 
  2. Failure: test store and access of phase (@test_phase.R#32) 
  3. Failure: test store and access of phase (@test_phase.R#36) 
  4. Failure: test store and access of phase (@test_phase.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

Installation output

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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/3.6/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)

Tests output


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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, 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, rowsum

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
── 1. Failure: test store and access of phase (@test_phase.R#31)  ──────────────
`x` not equal to `expected`.
4/4 mismatches
x[1]: "1/0"
y[1]: "1|1"

x[2]: "1|1"
y[2]: "0/0"

x[3]: "0|1"
y[3]: "1/0"

x[4]: "0|1"
y[4]: "1/0"

── 2. Failure: test store and access of phase (@test_phase.R#32)  ──────────────
`x` not equal to `expected`.
3/4 mismatches
x[1]: "1|0"
y[1]: "0/0"

x[2]: "0/1"
y[2]: "0|1"

x[3]: "0|1"
y[3]: "0|0"

── 3. Failure: test store and access of phase (@test_phase.R#36)  ──────────────
`x` not equal to `expected`.
3/4 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1
[4] 0 - 1 == -1

── 4. Failure: test store and access of phase (@test_phase.R#37)  ──────────────
`x` not equal to `expected`.
2/4 mismatches (average diff: 1)
[1] 1 - 0 ==  1
[2] 0 - 1 == -1

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 92 SKIPPED: 1 FAILED: 4
1. Failure: test store and access of phase (@test_phase.R#31) 
2. Failure: test store and access of phase (@test_phase.R#32) 
3. Failure: test store and access of phase (@test_phase.R#36) 
4. Failure: test store and access of phase (@test_phase.R#37) 

Error: testthat unit tests failed
Execution halted

Example timings

name	user	system	elapsed
ASEset-barplot	0.369	0.010	0.383
ASEset-class	0.584	0.036	0.631
ASEset-filters	0.089	0.003	0.091
ASEset-gbarplot	0.080	0.002	0.082
ASEset-glocationplot	5.505	0.185	5.738
ASEset-gviztrack	0.714	0.073	0.796
ASEset-scanForHeterozygotes	1.908	0.017	1.939
ASEset.old	0.000	0.001	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.003	0.003	0.005
DetectedAI-class	0.216	0.002	0.223
DetectedAI-plot	2.086	0.013	2.128
DetectedAI-summary	0.192	0.006	0.200
GRvariants	0.002	0.002	0.005
GlobalAnalysis-class	0.002	0.002	0.003
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.457	0.008	2.488
RegionSummary-class	0.001	0.000	0.001
RiskVariant-class	0	0	0
annotation-wrappers	6.326	0.571	7.719
annotationBarplot	0	0	0
barplot-lattice-support	0.232	0.001	0.237
binom.test	0.102	0.002	0.104
chisq.test	0.229	0.004	0.233
cigar-utilities	0.01	0.00	0.01
countAllelesFromBam	0.002	0.001	0.003
coverageMatrixListFromGAL	0.856	0.044	0.906
decorateWithExons	0.002	0.002	0.004
decorateWithGenes	0.002	0.002	0.004
defaultMapBias	0.039	0.003	0.042
defaultPhase	0.001	0.000	0.002
detectAI	0.189	0.002	0.192
fractionPlotDf	0.040	0.001	0.041
gba	0.000	0.000	0.001
genomatrix	0	0	0
genotype2phase	0.036	0.004	0.041
getAlleleCounts	3.978	0.029	4.041
getAlleleQuality	3.359	0.049	3.435
getAreaFromGeneNames	0.288	0.006	0.296
getDefaultMapBiasExpMean	0.040	0.002	0.041
getSnpIdFromLocation	21.861	1.516	23.467
histplot	0.000	0.001	0.000
implodeList-old	0.007	0.000	0.006
import-bam-2	0.008	0.000	0.008
import-bam	18.981	0.384	19.502
import-bcf	0.896	0.023	0.923
inferAlleles	0.039	0.002	0.041
inferAltAllele	0.035	0.002	0.038
inferGenotypes	0.068	0.001	0.069
initialize-ASEset	0.064	0.000	0.064
initialize-DetectedAI	0.137	0.002	0.139
initialize-GlobalAnalysis	0.006	0.003	0.007
initialize-RiskVariant	0.002	0.002	0.004
legendBarplot	0	0	0
locationplot	1.929	0.053	1.986
lva	9.783	0.020	9.862
lva.internal	0.372	0.002	0.375
makeMaskedFasta	0.932	0.005	0.940
mapBiasRef	0.023	0.003	0.026
minCountFilt	0.140	0.002	0.144
minFreqFilt	0.156	0.001	0.158
multiAllelicFilt	0.043	0.002	0.045
phase2genotype	0.053	0.005	0.059
phaseArray2phaseMatrix	0.007	0.003	0.010
phaseMatrix2Array	0.005	0.001	0.007
randomRef	0.045	0.001	0.047
reads	0	0	0
refAllele	0.018	0.003	0.021
regionSummary	0.598	0.004	0.609
scanForHeterozygotes-old	3.947	0.017	3.991

CHECK report for AllelicImbalance on merida2

Summary

Command output

Installation output

Tests output

Example timings