Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for AllelicImbalance on merida1

This page was generated on 2020-08-07 12:28:56 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AllelicImbalance PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 42/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.27.0
Jesper R Gadin
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: master
Last Commit: 053ddfb
Last Changed Date: 2020-04-27 14:36:41 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.27.0
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_1.27.0.tar.gz
StartedAt: 2020-08-07 00:13:37 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 00:23:22 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 584.9 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.27.0’
* 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 (user + system) or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     26.795  1.553  28.535
import-bam               23.022  0.327  23.429
lva                      16.471  0.042  16.528
scanForHeterozygotes-old  7.648  0.024   7.682
annotation-wrappers       6.981  0.290   7.284
getAlleleCounts           6.577  0.030   6.619
getAlleleQuality          6.431  0.023   6.462
ASEset-glocationplot      5.578  0.112   5.698
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.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: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

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 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:base':

    strsplit

Loading required package: Rsamtools
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 23.027   0.936  23.972 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.4280.0380.467
ASEset-class0.7180.0060.725
ASEset-filters0.1010.0050.106
ASEset-gbarplot0.0790.0040.083
ASEset-glocationplot5.5780.1125.698
ASEset-gviztrack0.9060.0900.997
ASEset-scanForHeterozygotes3.1580.0283.192
ASEset.old0.0000.0000.001
ASEset.sim000
ASEsetFromBam0.0010.0020.003
DetectedAI-class0.1340.0030.137
DetectedAI-plot1.9110.0191.933
DetectedAI-summary0.1900.0110.201
GRvariants0.0020.0040.006
GlobalAnalysis-class0.0010.0020.004
LinkVariantAlmlof-class0.0010.0000.000
LinkVariantAlmlof-plot3.4420.0143.462
RegionSummary-class0.0000.0000.001
RiskVariant-class000
annotation-wrappers6.9810.2907.284
annotationBarplot0.0010.0000.001
barplot-lattice-support0.1810.0020.183
binom.test0.0930.0040.097
chisq.test0.2510.0060.259
cigar-utilities0.0130.0000.013
countAllelesFromBam0.0020.0030.005
coverageMatrixListFromGAL1.1780.0181.197
decorateWithExons0.0010.0020.003
decorateWithGenes0.0010.0020.003
defaultMapBias0.0580.0040.063
defaultPhase0.0010.0010.002
detectAI0.1540.0070.161
fractionPlotDf0.0570.0060.063
gba000
genomatrix0.0000.0010.000
genotype2phase0.0500.0050.056
getAlleleCounts6.5770.0306.619
getAlleleQuality6.4310.0236.462
getAreaFromGeneNames0.520.010.53
getDefaultMapBiasExpMean0.0920.0030.096
getSnpIdFromLocation26.795 1.55328.535
histplot000
implodeList-old0.0090.0010.010
import-bam-20.0120.0000.013
import-bam23.022 0.32723.429
import-bcf1.1440.0261.171
inferAlleles0.0230.0040.028
inferAltAllele0.0280.0040.032
inferGenotypes0.0530.0030.056
initialize-ASEset0.1310.0020.133
initialize-DetectedAI0.1700.0030.174
initialize-GlobalAnalysis0.0040.0020.006
initialize-RiskVariant0.0010.0020.003
legendBarplot0.0010.0000.001
locationplot2.6050.0412.651
lva16.471 0.04216.528
lva.internal0.5790.0040.584
makeMaskedFasta1.0680.0061.077
mapBiasRef0.0320.0030.035
minCountFilt0.1300.0030.134
minFreqFilt0.1210.0040.125
multiAllelicFilt0.0260.0050.030
phase2genotype0.0410.0060.047
phaseArray2phaseMatrix0.0140.0030.016
phaseMatrix2Array0.0110.0030.013
randomRef0.0340.0020.036
reads0.0000.0010.000
refAllele0.0300.0040.033
regionSummary0.9920.0040.997
scanForHeterozygotes-old7.6480.0247.682