Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:07:36 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for AllelicImbalance on machv2


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 42/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.32.0  (landing page)
Jesper R Gadin
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: RELEASE_3_14
git_last_commit: 428ab8c
git_last_commit_date: 2021-10-26 12:10:09 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AllelicImbalance
Version: 1.32.0
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_1.32.0.tar.gz
StartedAt: 2022-01-25 10:01:57 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 10:15:28 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 811.0 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.32.0’
* 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                      150.533  0.344 151.055
getSnpIdFromLocation      30.076  1.674  31.770
LinkVariantAlmlof-plot    31.371  0.102  31.508
import-bam                25.746  0.327  26.115
scanForHeterozygotes-old  10.003  0.028  10.045
annotation-wrappers        7.718  0.266   8.000
ASEset-glocationplot       6.778  0.115   6.898
getAlleleCounts            6.850  0.019   6.873
getAlleleQuality           6.096  0.023   6.142
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 27.969   1.133  29.121 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.5600.0410.602
ASEset-class0.9180.0120.930
ASEset-filters0.1660.0160.183
ASEset-gbarplot0.1430.0180.161
ASEset-glocationplot6.7780.1156.898
ASEset-gviztrack1.0530.0401.094
ASEset-scanForHeterozygotes2.9720.0192.993
ASEset.old0.0000.0010.000
ASEset.sim0.0000.0000.001
ASEsetFromBam0.0030.0030.006
DetectedAI-class0.4360.0060.443
DetectedAI-plot2.8740.0322.916
DetectedAI-summary0.4630.0150.480
GRvariants0.0020.0030.005
GlobalAnalysis-class0.0020.0030.004
LinkVariantAlmlof-class0.0000.0010.000
LinkVariantAlmlof-plot31.371 0.10231.508
RegionSummary-class000
RiskVariant-class000
annotation-wrappers7.7180.2668.000
annotationBarplot0.0000.0010.000
barplot-lattice-support0.3190.0030.322
binom.test0.2510.0060.256
chisq.test0.4530.0080.461
cigar-utilities0.0170.0010.018
countAllelesFromBam0.0010.0030.005
coverageMatrixListFromGAL1.6110.0171.630
decorateWithExons0.0010.0030.004
decorateWithGenes0.0020.0030.003
defaultMapBias0.0810.0050.086
defaultPhase0.0010.0010.001
detectAI0.4080.0040.411
fractionPlotDf0.1110.0040.115
gba0.0000.0010.001
genomatrix000
genotype2phase0.0530.0070.060
getAlleleCounts6.8500.0196.873
getAlleleQuality6.0960.0236.142
getAreaFromGeneNames0.6150.0080.623
getDefaultMapBiasExpMean0.0910.0040.095
getSnpIdFromLocation30.076 1.67431.770
histplot000
implodeList-old0.0100.0000.011
import-bam-20.0290.0010.030
import-bam25.746 0.32726.115
import-bcf1.2740.0251.300
inferAlleles0.0350.0030.039
inferAltAllele0.0660.0040.070
inferGenotypes0.1290.0030.132
initialize-ASEset0.2140.0010.216
initialize-DetectedAI0.4240.0040.429
initialize-GlobalAnalysis0.0040.0040.009
initialize-RiskVariant0.0010.0020.003
legendBarplot0.0010.0000.000
locationplot3.4250.0513.478
lva150.533 0.344151.055
lva.internal1.1920.0051.198
makeMaskedFasta1.1650.0131.179
mapBiasRef0.0630.0030.067
minCountFilt0.1920.0050.197
minFreqFilt0.1890.0050.194
multiAllelicFilt0.0320.0060.066
phase2genotype0.0530.0040.057
phaseArray2phaseMatrix0.0310.0020.034
phaseMatrix2Array0.0300.0020.032
randomRef0.0470.0020.049
reads0.0000.0000.001
refAllele0.0420.0040.047
regionSummary2.3100.0382.350
scanForHeterozygotes-old10.003 0.02810.045