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This page was generated on 2022-12-01 11:09:20 -0500 (Thu, 01 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4203
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
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 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? 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 39/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.37.0  (landing page)
Jesper R Gadin
Snapshot Date: 2022-11-30 14:00:15 -0500 (Wed, 30 Nov 2022)
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: master
git_last_commit: 330d8ed
git_last_commit_date: 2022-11-01 11:08:46 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'GenomicAlignments' which is not available

Summary

Package: AllelicImbalance
Version: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2022-11-30 22:19:50 -0500 (Wed, 30 Nov 2022)
EndedAt: 2022-11-30 22:37:57 -0500 (Wed, 30 Nov 2022)
EllapsedTime: 1086.3 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_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2022-11-13 r83342)
* 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 ‘1.37.0’
* 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
getSnpIdFromLocation        35.361  1.952  50.021
import-bam                  29.063  0.427  38.791
lva                         21.114  0.056  27.589
scanForHeterozygotes-old    11.415  0.038  14.860
getAlleleCounts              9.162  0.064  12.344
annotation-wrappers          8.196  0.369  11.183
getAlleleQuality             8.163  0.034  10.761
ASEset-glocationplot         7.304  0.066   9.645
LinkVariantAlmlof-plot       4.763  0.019   6.232
ASEset-scanForHeterozygotes  3.902  0.027   5.145
* 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/4.3/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 Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences"
Copyright (C) 2022 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, aperm, 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 
 34.447   1.379  46.748 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.3820.0170.512
ASEset-class0.9900.1181.447
ASEset-filters0.1160.0160.173
ASEset-gbarplot0.0840.0120.123
ASEset-glocationplot7.3040.0669.645
ASEset-gviztrack1.1620.0671.624
ASEset-scanForHeterozygotes3.9020.0275.145
ASEset.old000
ASEset.sim0.0000.0000.001
ASEsetFromBam0.0010.0030.005
DetectedAI-class0.2110.0040.287
DetectedAI-plot3.0000.0193.940
DetectedAI-summary0.2630.0080.347
GRvariants0.0010.0030.004
GlobalAnalysis-class0.0020.0030.009
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot4.7630.0196.232
RegionSummary-class0.0010.0000.000
RiskVariant-class0.0010.0000.002
annotation-wrappers 8.196 0.36911.183
annotationBarplot0.0000.0000.001
barplot-lattice-support0.2580.0020.339
binom.test0.1060.0030.142
chisq.test0.3060.0040.401
cigar-utilities0.0220.0010.033
countAllelesFromBam0.0020.0030.007
coverageMatrixListFromGAL1.7450.0112.302
decorateWithExons0.0020.0020.008
decorateWithGenes0.0020.0030.006
defaultMapBias0.0710.0040.094
defaultPhase0.0020.0000.002
detectAI0.2030.0040.257
fractionPlotDf0.0670.0040.087
gba000
genomatrix0.0000.0010.000
genotype2phase0.0560.0060.080
getAlleleCounts 9.162 0.06412.344
getAlleleQuality 8.163 0.03410.761
getAreaFromGeneNames0.7230.0100.988
getDefaultMapBiasExpMean0.0530.0030.071
getSnpIdFromLocation35.361 1.95250.021
histplot000
implodeList-old0.0100.0000.013
import-bam-20.0180.0000.026
import-bam29.063 0.42738.791
import-bcf1.4450.0251.914
inferAlleles0.0240.0030.032
inferAltAllele0.0320.0030.047
inferGenotypes0.0670.0030.084
initialize-ASEset0.1700.0020.225
initialize-DetectedAI0.1980.0040.266
initialize-GlobalAnalysis0.0020.0030.005
initialize-RiskVariant0.0020.0030.005
legendBarplot000
locationplot3.2770.0274.358
lva21.114 0.05627.589
lva.internal0.7290.0060.975
makeMaskedFasta1.2880.0071.680
mapBiasRef0.0250.0030.040
minCountFilt0.1480.0040.197
minFreqFilt0.1460.0030.194
multiAllelicFilt0.0230.0040.037
phase2genotype0.0460.0060.065
phaseArray2phaseMatrix0.0080.0030.018
phaseMatrix2Array0.0060.0030.013
randomRef0.0400.0020.054
reads0.0000.0000.001
refAllele0.0280.0040.046
regionSummary1.2610.0061.658
scanForHeterozygotes-old11.415 0.03814.860