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This page was generated on 2021-09-20 15:04:43 -0400 (Mon, 20 Sep 2021).

CHECK results for AllelicImbalance on nebbiolo1

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raw results

Package 44/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.30.0  (landing page)
Jesper R Gadin
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: RELEASE_3_13
git_last_commit: 5e00a1f
git_last_commit_date: 2021-05-19 12:00:58 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.30.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AllelicImbalance_1.30.0.tar.gz
StartedAt: 2021-09-19 08:48:18 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 08:57:32 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 553.9 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AllelicImbalance_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.30.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
lva                      120.598  0.359 120.965
import-bam                27.156  0.172  27.341
LinkVariantAlmlof-plot    26.890  0.347  27.240
getSnpIdFromLocation      19.117  1.412  20.532
ASEset-glocationplot       4.941  0.175   5.117
scanForHeterozygotes-old   5.111  0.000   5.111
* 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:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 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 
 17.615   0.761  18.362 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.4290.0160.444
ASEset-class1.4430.0441.487
ASEset-filters0.0820.0000.082
ASEset-gbarplot0.0890.0000.088
ASEset-glocationplot4.9410.1755.117
ASEset-gviztrack0.6170.1010.716
ASEset-scanForHeterozygotes1.8780.0951.975
ASEset.old000
ASEset.sim0.0000.0000.001
ASEsetFromBam0.0010.0000.002
DetectedAI-class0.1930.0070.201
DetectedAI-plot1.5750.0801.655
DetectedAI-summary0.2440.0600.303
GRvariants0.0010.0010.002
GlobalAnalysis-class0.0010.0000.001
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot26.890 0.34727.240
RegionSummary-class000
RiskVariant-class000
annotation-wrappers3.9390.2994.237
annotationBarplot000
barplot-lattice-support0.1730.0000.174
binom.test0.1040.0000.104
chisq.test0.2280.0000.228
cigar-utilities0.0120.0000.012
countAllelesFromBam0.0020.0000.001
coverageMatrixListFromGAL1.9270.5482.476
decorateWithExons0.0030.0000.002
decorateWithGenes0.0020.0000.001
defaultMapBias0.0360.0040.040
defaultPhase0.0010.0000.001
detectAI0.1930.0000.193
fractionPlotDf0.0590.0000.058
gba0.0010.0000.000
genomatrix000
genotype2phase0.0290.0000.029
getAlleleCounts3.7980.0083.807
getAlleleQuality3.5620.0243.586
getAreaFromGeneNames0.3070.0080.315
getDefaultMapBiasExpMean0.0390.0000.040
getSnpIdFromLocation19.117 1.41220.532
histplot0.0000.0000.001
implodeList-old0.0050.0000.005
import-bam-20.0130.0000.013
import-bam27.156 0.17227.341
import-bcf1.2680.0121.281
inferAlleles0.0190.0000.018
inferAltAllele0.0280.0000.028
inferGenotypes0.0560.0000.056
initialize-ASEset0.0920.0000.091
initialize-DetectedAI0.1820.0040.186
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0020.0000.001
legendBarplot0.0000.0010.000
locationplot1.7160.0031.718
lva120.598 0.359120.965
lva.internal0.6670.0000.667
makeMaskedFasta1.2490.0001.250
mapBiasRef0.0350.0000.035
minCountFilt0.0880.0030.092
minFreqFilt0.0920.0030.095
multiAllelicFilt0.0180.0000.018
phase2genotype0.0350.0040.039
phaseArray2phaseMatrix0.0170.0030.021
phaseMatrix2Array0.0210.0000.021
randomRef0.0320.0000.032
reads0.0000.0010.000
refAllele0.0140.0070.021
regionSummary1.2150.0001.216
scanForHeterozygotes-old5.1110.0005.111