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CHECK report for AllelicImbalance on veracruz1

This page was generated on 2018-04-12 13:37:32 -0400 (Thu, 12 Apr 2018).

Package 35/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.16.0
Jesper R Gadin
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_6
Last Commit: 85f652a
Last Changed Date: 2017-10-30 12:40:08 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz
StartedAt: 2018-04-12 00:15:58 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:23:10 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 432.5 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.16.0’
* 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 20.328  1.525  22.189
import-bam           13.808  0.340  14.394
annotation-wrappers   7.789  0.228   8.159
lva                   6.101  0.017   6.224
ASEset-glocationplot  5.657  0.023   5.789
* 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


Installation output

AllelicImbalance.Rcheck/00install.out

* 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)

Tests output

AllelicImbalance.Rcheck/tests/test-all.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    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 
 17.497   0.495  18.541 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot1.0230.0061.046
ASEset-class0.8190.0440.873
ASEset-filters0.1150.0040.118
ASEset-gbarplot0.0330.0020.035
ASEset-glocationplot5.6570.0235.789
ASEset-gviztrack0.8640.0470.918
ASEset-scanForHeterozygotes2.3340.0272.395
ASEset.old0.0010.0000.001
ASEset.sim0.0010.0000.001
ASEsetFromBam0.0020.0010.003
DetectedAI-class0.0650.0010.070
DetectedAI-plot1.970.012.00
DetectedAI-summary0.1100.0050.115
GRvariants0.0020.0020.004
GlobalAnalysis-class0.0020.0010.003
LinkVariantAlmlof-class0.0000.0000.001
LinkVariantAlmlof-plot1.7880.0051.820
RegionSummary-class0.0010.0000.000
RiskVariant-class0.0010.0000.000
annotation-wrappers7.7890.2288.159
annotationBarplot0.0010.0000.000
barplot-lattice-support0.1720.0010.184
binom.test0.0330.0020.034
chisq.test0.0820.0020.084
cigar-utilities0.0140.0010.014
countAllelesFromBam0.0030.0020.005
coverageMatrixListFromGAL1.0010.0271.048
decorateWithExons0.0030.0010.004
decorateWithGenes0.0030.0010.004
defaultMapBias0.0530.0030.055
defaultPhase0.0010.0000.002
detectAI0.0600.0020.062
fractionPlotDf0.0300.0020.032
gba0.0000.0000.001
genomatrix0.0000.0000.001
genotype2phase0.0380.0040.043
getAlleleCounts4.5760.0184.654
getAlleleQuality4.5580.0144.653
getAreaFromGeneNames0.4020.0100.414
getDefaultMapBiasExpMean0.0270.0020.029
getSnpIdFromLocation20.328 1.52522.189
histplot0.0010.0000.000
implodeList-old0.0080.0000.008
import-bam-20.0090.0000.009
import-bam13.808 0.34014.394
import-bcf0.6470.0240.680
inferAlleles0.0860.0010.089
inferAltAllele0.0150.0010.017
inferGenotypes0.0860.0020.093
initialize-ASEset0.2210.0010.234
initialize-DetectedAI0.0550.0020.056
initialize-GlobalAnalysis0.0060.0020.008
initialize-RiskVariant0.0020.0020.004
legendBarplot0.0010.0010.001
locationplot1.7590.0171.810
lva6.1010.0176.224
lva.internal0.7880.0040.802
makeMaskedFasta0.5850.0040.599
mapBiasRef0.0120.0020.014
minCountFilt0.0350.0020.043
minFreqFilt0.0330.0020.036
multiAllelicFilt0.0100.0020.012
phase2genotype0.0150.0020.017
phaseArray2phaseMatrix0.0060.0010.007
phaseMatrix2Array0.0080.0020.009
randomRef0.0120.0010.014
reads000
refAllele0.0150.0010.016
regionSummary0.4220.0040.438
scanForHeterozygotes-old4.4900.0204.598