Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:03:26 -0400 (Wed, 16 Oct 2019).
Package 43/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
AllelicImbalance 1.22.0 Jesper R Gadin
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: AllelicImbalance |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings AllelicImbalance_1.22.0.tar.gz |
StartedAt: 2019-10-15 23:41:55 -0400 (Tue, 15 Oct 2019) |
EndedAt: 2019-10-15 23:49:09 -0400 (Tue, 15 Oct 2019) |
EllapsedTime: 434.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AllelicImbalance.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings AllelicImbalance_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.22.0’ * 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 or elapsed time > 5s user system elapsed getSnpIdFromLocation 25.020 1.063 26.153 import-bam 20.917 0.120 21.740 lva 8.621 0.008 8.637 * 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-3.9-bioc/R/bin/R CMD INSTALL AllelicImbalance ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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, 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: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum Loading required package: GenomicAlignments Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ] > > > > proc.time() user system elapsed 16.197 0.575 16.792
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
name | user | system | elapsed | |
ASEset-barplot | 0.264 | 0.000 | 0.264 | |
ASEset-class | 1.099 | 0.020 | 1.118 | |
ASEset-filters | 0.075 | 0.000 | 0.075 | |
ASEset-gbarplot | 0.083 | 0.000 | 0.083 | |
ASEset-glocationplot | 4.454 | 0.080 | 4.535 | |
ASEset-gviztrack | 0.471 | 0.000 | 0.472 | |
ASEset-scanForHeterozygotes | 1.337 | 0.000 | 1.337 | |
ASEset.old | 0 | 0 | 0 | |
ASEset.sim | 0 | 0 | 0 | |
ASEsetFromBam | 0.001 | 0.000 | 0.002 | |
DetectedAI-class | 0.136 | 0.000 | 0.136 | |
DetectedAI-plot | 1.316 | 0.000 | 1.315 | |
DetectedAI-summary | 0.131 | 0.000 | 0.130 | |
GRvariants | 0.002 | 0.000 | 0.001 | |
GlobalAnalysis-class | 0.001 | 0.000 | 0.001 | |
LinkVariantAlmlof-class | 0.000 | 0.000 | 0.001 | |
LinkVariantAlmlof-plot | 1.613 | 0.000 | 1.613 | |
RegionSummary-class | 0 | 0 | 0 | |
RiskVariant-class | 0.001 | 0.000 | 0.000 | |
annotation-wrappers | 4.666 | 0.160 | 4.838 | |
annotationBarplot | 0 | 0 | 0 | |
barplot-lattice-support | 0.154 | 0.000 | 0.155 | |
binom.test | 0.080 | 0.000 | 0.081 | |
chisq.test | 0.249 | 0.008 | 0.260 | |
cigar-utilities | 0.016 | 0.000 | 0.016 | |
countAllelesFromBam | 0.002 | 0.000 | 0.002 | |
coverageMatrixListFromGAL | 0.745 | 0.003 | 0.748 | |
decorateWithExons | 0.002 | 0.000 | 0.002 | |
decorateWithGenes | 0.001 | 0.000 | 0.002 | |
defaultMapBias | 0.028 | 0.000 | 0.040 | |
defaultPhase | 0 | 0 | 0 | |
detectAI | 0.149 | 0.000 | 0.149 | |
fractionPlotDf | 0.046 | 0.000 | 0.046 | |
gba | 0 | 0 | 0 | |
genomatrix | 0.000 | 0.000 | 0.001 | |
genotype2phase | 0.027 | 0.000 | 0.027 | |
getAlleleCounts | 3.819 | 0.004 | 3.822 | |
getAlleleQuality | 4.156 | 0.008 | 4.164 | |
getAreaFromGeneNames | 0.417 | 0.000 | 0.418 | |
getDefaultMapBiasExpMean | 0.061 | 0.000 | 0.061 | |
getSnpIdFromLocation | 25.020 | 1.063 | 26.153 | |
histplot | 0 | 0 | 0 | |
implodeList-old | 0.005 | 0.000 | 0.005 | |
import-bam-2 | 0.005 | 0.000 | 0.005 | |
import-bam | 20.917 | 0.120 | 21.740 | |
import-bcf | 0.911 | 0.020 | 0.941 | |
inferAlleles | 0.022 | 0.000 | 0.022 | |
inferAltAllele | 0.025 | 0.000 | 0.025 | |
inferGenotypes | 0.046 | 0.000 | 0.046 | |
initialize-ASEset | 0.05 | 0.00 | 0.05 | |
initialize-DetectedAI | 0.103 | 0.000 | 0.103 | |
initialize-GlobalAnalysis | 0.004 | 0.000 | 0.004 | |
initialize-RiskVariant | 0.001 | 0.000 | 0.002 | |
legendBarplot | 0 | 0 | 0 | |
locationplot | 1.455 | 0.000 | 1.455 | |
lva | 8.621 | 0.008 | 8.637 | |
lva.internal | 0.339 | 0.000 | 0.340 | |
makeMaskedFasta | 1.007 | 0.000 | 1.012 | |
mapBiasRef | 0.027 | 0.000 | 0.030 | |
minCountFilt | 0.140 | 0.004 | 0.145 | |
minFreqFilt | 0.129 | 0.000 | 0.129 | |
multiAllelicFilt | 0.026 | 0.000 | 0.026 | |
phase2genotype | 0.043 | 0.000 | 0.042 | |
phaseArray2phaseMatrix | 0.005 | 0.000 | 0.005 | |
phaseMatrix2Array | 0.005 | 0.000 | 0.004 | |
randomRef | 0.029 | 0.000 | 0.029 | |
reads | 0.001 | 0.000 | 0.000 | |
refAllele | 0.011 | 0.000 | 0.011 | |
regionSummary | 0.444 | 0.000 | 0.444 | |
scanForHeterozygotes-old | 3.379 | 0.000 | 3.380 | |