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This page was generated on 2021-01-24 11:49:11 -0500 (Sun, 24 Jan 2021).
TO THE DEVELOPERS/MAINTAINERS OF THE AllelicImbalance PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 44/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
AllelicImbalance 1.28.0 Jesper R Gadin
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | [ OK ] | ![]() | ||||||
nebbiolo1 | Linux (Ubuntu 20.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | ERROR |
Package: AllelicImbalance |
Version: 1.28.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AllelicImbalance_1.28.0.tar.gz |
StartedAt: 2021-01-23 23:15:26 -0500 (Sat, 23 Jan 2021) |
EndedAt: 2021-01-23 23:24:50 -0500 (Sat, 23 Jan 2021) |
EllapsedTime: 563.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AllelicImbalance.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AllelicImbalance_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/AllelicImbalance.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.28.0’ * 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 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 25.836 0.148 26.663 getSnpIdFromLocation 24.180 1.056 25.321 lva 14.284 0.008 14.317 annotation-wrappers 6.852 0.164 7.180 scanForHeterozygotes-old 6.156 0.000 6.165 getAlleleCounts 5.676 0.012 5.700 ASEset-glocationplot 5.624 0.028 5.665 * 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
AllelicImbalance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL AllelicImbalance ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-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)
AllelicImbalance.Rcheck/tests/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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 object is masked from 'package:base': expand.grid 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:base': strsplit Loading required package: Rsamtools ══ Skipped tests ═══════════════════════════════════════════════════════════════ ● empty test (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ] > > > > proc.time() user system elapsed 22.864 0.520 24.934
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
name | user | system | elapsed | |
ASEset-barplot | 0.380 | 0.004 | 0.387 | |
ASEset-class | 0.528 | 0.020 | 0.551 | |
ASEset-filters | 0.100 | 0.008 | 0.105 | |
ASEset-gbarplot | 0.076 | 0.008 | 0.085 | |
ASEset-glocationplot | 5.624 | 0.028 | 5.665 | |
ASEset-gviztrack | 0.680 | 0.040 | 0.723 | |
ASEset-scanForHeterozygotes | 2.004 | 0.000 | 2.003 | |
ASEset.old | 0 | 0 | 0 | |
ASEset.sim | 0 | 0 | 0 | |
ASEsetFromBam | 0.000 | 0.000 | 0.002 | |
DetectedAI-class | 0.112 | 0.000 | 0.112 | |
DetectedAI-plot | 1.440 | 0.012 | 1.452 | |
DetectedAI-summary | 0.148 | 0.008 | 0.156 | |
GRvariants | 0.000 | 0.000 | 0.001 | |
GlobalAnalysis-class | 0.004 | 0.000 | 0.001 | |
LinkVariantAlmlof-class | 0 | 0 | 0 | |
LinkVariantAlmlof-plot | 4.256 | 0.008 | 4.281 | |
RegionSummary-class | 0.000 | 0.000 | 0.001 | |
RiskVariant-class | 0 | 0 | 0 | |
annotation-wrappers | 6.852 | 0.164 | 7.180 | |
annotationBarplot | 0 | 0 | 0 | |
barplot-lattice-support | 0.240 | 0.000 | 0.237 | |
binom.test | 0.112 | 0.000 | 0.110 | |
chisq.test | 0.28 | 0.00 | 0.28 | |
cigar-utilities | 0.016 | 0.004 | 0.019 | |
countAllelesFromBam | 0.000 | 0.000 | 0.002 | |
coverageMatrixListFromGAL | 1.372 | 0.004 | 1.385 | |
decorateWithExons | 0.000 | 0.004 | 0.002 | |
decorateWithGenes | 0.000 | 0.000 | 0.002 | |
defaultMapBias | 0.060 | 0.000 | 0.076 | |
defaultPhase | 0.004 | 0.000 | 0.001 | |
detectAI | 0.176 | 0.000 | 0.177 | |
fractionPlotDf | 0.060 | 0.000 | 0.058 | |
gba | 0 | 0 | 0 | |
genomatrix | 0 | 0 | 0 | |
genotype2phase | 0.028 | 0.000 | 0.028 | |
getAlleleCounts | 5.676 | 0.012 | 5.700 | |
getAlleleQuality | 4.536 | 0.000 | 4.542 | |
getAreaFromGeneNames | 0.404 | 0.000 | 0.407 | |
getDefaultMapBiasExpMean | 0.052 | 0.000 | 0.054 | |
getSnpIdFromLocation | 24.180 | 1.056 | 25.321 | |
histplot | 0 | 0 | 0 | |
implodeList-old | 0.004 | 0.000 | 0.005 | |
import-bam-2 | 0.008 | 0.000 | 0.008 | |
import-bam | 25.836 | 0.148 | 26.663 | |
import-bcf | 1.284 | 0.004 | 1.308 | |
inferAlleles | 0.016 | 0.004 | 0.022 | |
inferAltAllele | 0.036 | 0.000 | 0.037 | |
inferGenotypes | 0.064 | 0.000 | 0.063 | |
initialize-ASEset | 0.136 | 0.004 | 0.138 | |
initialize-DetectedAI | 0.180 | 0.000 | 0.182 | |
initialize-GlobalAnalysis | 0.004 | 0.000 | 0.006 | |
initialize-RiskVariant | 0.004 | 0.000 | 0.002 | |
legendBarplot | 0 | 0 | 0 | |
locationplot | 2.292 | 0.000 | 2.297 | |
lva | 14.284 | 0.008 | 14.317 | |
lva.internal | 0.548 | 0.000 | 0.549 | |
makeMaskedFasta | 1.188 | 0.000 | 1.189 | |
mapBiasRef | 0.02 | 0.00 | 0.02 | |
minCountFilt | 0.076 | 0.000 | 0.076 | |
minFreqFilt | 0.076 | 0.000 | 0.075 | |
multiAllelicFilt | 0.012 | 0.004 | 0.014 | |
phase2genotype | 0.024 | 0.000 | 0.025 | |
phaseArray2phaseMatrix | 0.008 | 0.000 | 0.008 | |
phaseMatrix2Array | 0.004 | 0.004 | 0.007 | |
randomRef | 0.020 | 0.000 | 0.022 | |
reads | 0 | 0 | 0 | |
refAllele | 0.016 | 0.000 | 0.016 | |
regionSummary | 0.612 | 0.000 | 0.612 | |
scanForHeterozygotes-old | 6.156 | 0.000 | 6.165 | |