Back to Multiple platform build/check report for BioC 3.19:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-28 17:39 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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

Package 54/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.42.0  (landing page)
Jesper R Gadin
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: RELEASE_3_19
git_last_commit: 4dc686c
git_last_commit_date: 2024-04-30 10:33:42 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for AllelicImbalance on nebbiolo1

To the developers/maintainers of the AllelicImbalance package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: AllelicImbalance
Version: 1.42.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AllelicImbalance_1.42.0.tar.gz
StartedAt: 2024-06-26 20:29:14 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 20:38:02 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 528.2 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AllelicImbalance_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.42.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN VERSION 1.12.0
* checking code 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 loading without being on the library search path ... 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
import-bam           22.181  0.400  22.588
getSnpIdFromLocation 16.327  1.892  18.223
lva                   7.639  0.016   7.654
ASEset-glocationplot  5.006  0.195   5.202
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.


Installation output

AllelicImbalance.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_utils.R:3:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.140   1.651  18.780 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.1530.0310.184
ASEset-class0.3980.0050.401
ASEset-filters0.0450.0000.045
ASEset-gbarplot0.0340.0000.034
ASEset-glocationplot5.0060.1955.202
ASEset-gviztrack0.4440.0880.533
ASEset-scanForHeterozygotes1.6100.1031.714
ASEset.old000
ASEset.sim0.0000.0000.001
ASEsetFromBam0.0020.0000.001
DetectedAI-class0.0790.0010.078
DetectedAI-plot1.1420.0191.161
DetectedAI-summary0.0970.0040.100
GRvariants0.0020.0000.001
GlobalAnalysis-class0.0010.0000.001
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.7620.0111.774
RegionSummary-class000
RiskVariant-class000
annotation-wrappers3.8550.3074.163
annotationBarplot000
barplot-lattice-support0.1030.0000.103
binom.test0.0410.0000.042
chisq.test0.1210.0040.125
cigar-utilities0.0130.0000.012
countAllelesFromBam0.0000.0020.001
coverageMatrixListFromGAL0.6670.0090.676
decorateWithExons0.0020.0000.001
decorateWithGenes0.0010.0000.001
defaultMapBias0.0320.0000.033
defaultPhase0.0010.0000.001
detectAI0.0740.0030.077
fractionPlotDf0.1790.0120.191
gba000
genomatrix000
genotype2phase0.0260.0000.025
getAlleleCounts3.5860.0763.662
getAlleleQuality3.1860.0123.199
getAreaFromGeneNames0.4590.0440.502
getDefaultMapBiasExpMean0.0230.0000.023
getSnpIdFromLocation16.327 1.89218.223
histplot0.0010.0000.000
implodeList-old0.0020.0040.005
import-bam-20.0080.0000.008
import-bam22.181 0.40022.588
import-bcf1.1190.0121.132
inferAlleles0.010.000.01
inferAltAllele0.0130.0000.013
inferGenotypes0.0240.0000.023
initialize-ASEset0.0650.0000.065
initialize-DetectedAI0.0720.0000.073
initialize-GlobalAnalysis0.0010.0000.001
initialize-RiskVariant0.0010.0000.001
legendBarplot000
locationplot1.2550.0271.283
lva7.6390.0167.654
lva.internal0.2700.0010.270
makeMaskedFasta1.0520.0311.084
mapBiasRef0.0100.0010.011
minCountFilt0.0570.0000.056
minFreqFilt0.0560.0000.056
multiAllelicFilt0.010.000.01
phase2genotype0.0190.0000.019
phaseArray2phaseMatrix0.0030.0000.004
phaseMatrix2Array0.0030.0000.003
randomRef0.0140.0000.015
reads0.0000.0000.001
refAllele0.0110.0000.012
regionSummary0.4610.0000.461
scanForHeterozygotes-old4.2810.0154.297