Back to Multiple platform build/check report for BioC 3.14
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-20 12:05:32 -0400 (Wed, 20 Oct 2021).

CHECK results for AllelicImbalance on merida1

To the developers/maintainers of the AllelicImbalance package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AllelicImbalance.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 42/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.31.0  (landing page)
Jesper R Gadin
Snapshot Date: 2021-10-19 14:50:04 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: master
git_last_commit: b838792
git_last_commit_date: 2021-05-19 12:00:58 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AllelicImbalance
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AllelicImbalance_1.31.0.tar.gz
StartedAt: 2021-10-20 00:30:16 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 00:42:13 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 716.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AllelicImbalance_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.31.0’
* 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 LazyData ... 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
lva                      127.468  0.379 128.041
getSnpIdFromLocation      24.529  1.305  25.912
LinkVariantAlmlof-plot    25.300  0.094  25.421
import-bam                22.584  0.304  22.942
scanForHeterozygotes-old   9.563  0.029   9.603
annotation-wrappers        5.638  0.522   6.735
ASEset-glocationplot       5.833  0.115   5.960
getAlleleCounts            5.823  0.025   5.859
getAlleleQuality           5.420  0.026   5.460
* 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/Resources/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    pattern

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

    strsplit

Loading required package: Rsamtools
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 24.075   1.051  25.122 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.5140.0420.557
ASEset-class0.8440.0070.854
ASEset-filters0.1560.0170.173
ASEset-gbarplot0.0940.0110.105
ASEset-glocationplot5.8330.1155.960
ASEset-gviztrack0.9180.0360.957
ASEset-scanForHeterozygotes2.5520.0212.577
ASEset.old000
ASEset.sim0.0000.0010.000
ASEsetFromBam0.0020.0030.005
DetectedAI-class0.3810.0050.387
DetectedAI-plot2.4400.0242.469
DetectedAI-summary0.3940.0070.402
GRvariants0.0010.0010.002
GlobalAnalysis-class0.0010.0020.003
LinkVariantAlmlof-class0.0000.0010.001
LinkVariantAlmlof-plot25.300 0.09425.421
RegionSummary-class0.0010.0000.000
RiskVariant-class0.0010.0000.000
annotation-wrappers5.6380.5226.735
annotationBarplot000
barplot-lattice-support0.2700.0030.274
binom.test0.1600.0030.164
chisq.test0.3580.0040.362
cigar-utilities0.0170.0010.018
countAllelesFromBam0.0010.0020.003
coverageMatrixListFromGAL1.1880.0091.198
decorateWithExons0.0020.0030.004
decorateWithGenes0.0010.0020.003
defaultMapBias0.0710.0040.076
defaultPhase0.0010.0010.002
detectAI0.3250.0060.333
fractionPlotDf0.0920.0030.094
gba000
genomatrix000
genotype2phase0.0550.0070.063
getAlleleCounts5.8230.0255.859
getAlleleQuality5.4200.0265.460
getAreaFromGeneNames0.5030.0080.512
getDefaultMapBiasExpMean0.0710.0030.074
getSnpIdFromLocation24.529 1.30525.912
histplot000
implodeList-old0.0060.0000.006
import-bam-20.0140.0010.014
import-bam22.584 0.30422.942
import-bcf1.1560.0191.178
inferAlleles0.0220.0020.024
inferAltAllele0.0550.0040.059
inferGenotypes0.0740.0040.077
initialize-ASEset0.1210.0000.121
initialize-DetectedAI0.3260.0050.331
initialize-GlobalAnalysis0.0040.0020.006
initialize-RiskVariant0.0020.0020.003
legendBarplot0.0000.0000.001
locationplot2.6410.0542.704
lva127.468 0.379128.041
lva.internal1.1480.0051.154
makeMaskedFasta1.1450.0071.152
mapBiasRef0.0650.0040.069
minCountFilt0.1690.0040.171
minFreqFilt0.1680.0030.172
multiAllelicFilt0.0290.0040.032
phase2genotype0.0770.0070.083
phaseArray2phaseMatrix0.0410.0030.043
phaseMatrix2Array0.0350.0030.038
randomRef0.0480.0020.050
reads000
refAllele0.0290.0030.032
regionSummary2.2500.0082.260
scanForHeterozygotes-old9.5630.0299.603