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CHECK report for AllelicImbalance on celaya2

This page was generated on 2019-10-16 12:52:06 -0400 (Wed, 16 Oct 2019).

Package 43/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.22.0
Jesper R Gadin
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_9
Last Commit: 04692e3
Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2019-10-16 00:28:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:39:04 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 645.8 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

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### Running 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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 44.777  4.108  49.369
import-bam           25.635  0.618  26.301
lva                  13.843  0.042  13.886
annotation-wrappers   6.023  0.600   6.624
ASEset-glocationplot  5.905  0.319   6.224
getAlleleCounts       6.065  0.033   6.097
getAlleleQuality      5.588  0.020   5.607
* 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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘AllelicImbalance’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AllelicImbalance)

Tests output

AllelicImbalance.Rcheck/tests/test-all.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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, 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
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 25.038   1.908  26.901 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.4840.0170.500
ASEset-class1.8080.0761.884
ASEset-filters0.1370.0050.142
ASEset-gbarplot0.0650.0040.069
ASEset-glocationplot5.9050.3196.224
ASEset-gviztrack0.6750.0240.701
ASEset-scanForHeterozygotes2.5010.0252.527
ASEset.old000
ASEset.sim0.0000.0010.001
ASEsetFromBam0.0030.0040.007
DetectedAI-class0.2510.0080.259
DetectedAI-plot2.7080.0212.732
DetectedAI-summary0.2870.0100.298
GRvariants0.0030.0030.005
GlobalAnalysis-class0.0020.0030.005
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot2.5660.0092.577
RegionSummary-class0.0000.0000.001
RiskVariant-class0.0010.0000.000
annotation-wrappers6.0230.6006.624
annotationBarplot0.0010.0000.001
barplot-lattice-support0.3160.0030.319
binom.test0.1650.0040.169
chisq.test0.3610.0090.371
cigar-utilities0.0200.0020.022
countAllelesFromBam0.0030.0040.008
coverageMatrixListFromGAL1.1320.0401.172
decorateWithExons0.0020.0030.005
decorateWithGenes0.0030.0050.008
defaultMapBias0.0550.0070.062
defaultPhase0.0020.0010.003
detectAI0.2650.0060.271
fractionPlotDf0.0770.0040.080
gba0.0000.0010.000
genomatrix0.0010.0000.001
genotype2phase0.0650.0080.072
getAlleleCounts6.0650.0336.097
getAlleleQuality5.5880.0205.607
getAreaFromGeneNames0.4820.0160.497
getDefaultMapBiasExpMean0.0790.0030.082
getSnpIdFromLocation44.777 4.10849.369
histplot0.0010.0000.001
implodeList-old0.0120.0000.012
import-bam-20.0120.0000.013
import-bam25.635 0.61826.301
import-bcf1.1770.0491.226
inferAlleles0.0400.0050.044
inferAltAllele0.0570.0050.062
inferGenotypes0.1100.0050.115
initialize-ASEset0.0730.0000.074
initialize-DetectedAI0.2700.0040.275
initialize-GlobalAnalysis0.0070.0050.012
initialize-RiskVariant0.0040.0050.007
legendBarplot0.0010.0010.000
locationplot2.6600.0502.711
lva13.843 0.04213.886
lva.internal0.5500.0060.555
makeMaskedFasta1.1390.0081.147
mapBiasRef0.0270.0030.029
minCountFilt0.1880.0030.191
minFreqFilt0.2200.0050.225
multiAllelicFilt0.0340.0030.038
phase2genotype0.0460.0060.051
phaseArray2phaseMatrix0.0080.0050.014
phaseMatrix2Array0.0060.0030.009
randomRef0.0540.0060.060
reads0.0000.0000.001
refAllele0.0250.0060.031
regionSummary0.6520.0050.657
scanForHeterozygotes-old4.7870.0824.870