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CHECK report for AllelicImbalance on merida1

This page was generated on 2019-04-16 11:57:11 -0400 (Tue, 16 Apr 2019).

Package 39/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.20.0
Jesper R Gadin
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_8
Last Commit: 4cd3a78
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2019-04-15 22:19:07 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:26:51 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 464.0 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 --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.20.0’
* 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 ... 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 24.518  1.816  26.574
import-bam           20.460  0.420  21.087
lva                  10.156  0.032  10.294
annotation-wrappers   5.242  0.248   5.523
* 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

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### Running command:
###
###   /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)

Tests output

AllelicImbalance.Rcheck/tests/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 
 18.721   0.859  19.748 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.3360.0090.346
ASEset-class0.6990.0920.799
ASEset-filters0.1080.0020.110
ASEset-gbarplot0.0940.0030.097
ASEset-glocationplot4.5510.0394.626
ASEset-gviztrack0.5990.0080.614
ASEset-scanForHeterozygotes1.9720.0141.995
ASEset.old000
ASEset.sim0.0000.0000.001
ASEsetFromBam0.0030.0020.005
DetectedAI-class0.2200.0030.224
DetectedAI-plot2.0440.0202.084
DetectedAI-summary0.1980.0050.205
GRvariants0.0010.0010.003
GlobalAnalysis-class0.0020.0020.003
LinkVariantAlmlof-class0.0000.0000.001
LinkVariantAlmlof-plot2.1830.0082.207
RegionSummary-class0.0010.0000.000
RiskVariant-class0.0010.0000.000
annotation-wrappers5.2420.2485.523
annotationBarplot0.0000.0010.000
barplot-lattice-support0.2160.0010.222
binom.test0.0910.0020.093
chisq.test0.2420.0020.245
cigar-utilities0.010.000.01
countAllelesFromBam0.0010.0010.003
coverageMatrixListFromGAL0.9930.0041.006
decorateWithExons0.0020.0010.003
decorateWithGenes0.0020.0020.005
defaultMapBias0.0350.0020.039
defaultPhase0.0010.0000.002
detectAI0.1870.0020.190
fractionPlotDf0.0610.0020.062
gba000
genomatrix0.0000.0000.001
genotype2phase0.0390.0030.042
getAlleleCounts4.7430.0174.794
getAlleleQuality4.6280.0144.687
getAreaFromGeneNames0.3940.0070.405
getDefaultMapBiasExpMean0.0550.0010.058
getSnpIdFromLocation24.518 1.81626.574
histplot000
implodeList-old0.0060.0010.006
import-bam-20.0110.0000.011
import-bam20.460 0.42021.087
import-bcf1.0000.0271.046
inferAlleles0.0410.0020.046
inferAltAllele0.0500.0010.052
inferGenotypes0.0890.0030.095
initialize-ASEset0.0750.0010.077
initialize-DetectedAI0.1680.0020.174
initialize-GlobalAnalysis0.0050.0010.006
initialize-RiskVariant0.0010.0010.003
legendBarplot0.0010.0000.001
locationplot2.6390.1452.811
lva10.156 0.03210.294
lva.internal0.3970.0040.404
makeMaskedFasta0.9270.0040.935
mapBiasRef0.0210.0030.024
minCountFilt0.1660.0020.170
minFreqFilt0.1420.0030.148
multiAllelicFilt0.0400.0030.045
phase2genotype0.0510.0050.057
phaseArray2phaseMatrix0.0100.0030.012
phaseMatrix2Array0.0060.0020.009
randomRef0.0450.0020.046
reads000
refAllele0.0130.0020.014
regionSummary0.7210.0020.730
scanForHeterozygotes-old4.2970.0234.365