Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:06:54 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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 |
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 41/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AllelicImbalance 1.33.1 (landing page) Jesper R Gadin
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: AllelicImbalance |
Version: 1.33.1 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AllelicImbalance.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AllelicImbalance_1.33.1.tar.gz |
StartedAt: 2022-03-17 18:25:36 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 18:31:59 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 382.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AllelicImbalance.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AllelicImbalance.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AllelicImbalance_1.33.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/AllelicImbalance.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'AllelicImbalance/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'AllelicImbalance' version '1.33.1' * 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 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 import-bam 21.36 0.42 21.78 getSnpIdFromLocation 13.70 2.02 15.72 lva 7.39 0.00 7.39 * 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: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL AllelicImbalance ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-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 converting help for package 'AllelicImbalance' finding HTML links ... done ASEset-barplot html ASEset-class html ASEset-filters html ASEset-gbarplot html ASEset-glocationplot html ASEset-gviztrack html ASEset-scanForHeterozygotes html ASEset.old html ASEset.sim html ASEsetFromBam html AllelicImbalance-package html DetectedAI-class html DetectedAI-plot html DetectedAI-summary html GRvariants html GlobalAnalysis-class html LinkVariantAlmlof-class html LinkVariantAlmlof-plot html RegionSummary-class html RiskVariant-class html annotation-wrappers html annotationBarplot html barplot-lattice-support html binom.test html chisq.test html cigar-utilities html countAllelesFromBam html coverageMatrixListFromGAL html decorateWithExons html decorateWithGenes html defaultMapBias html defaultPhase html detectAI html fractionPlotDf html gba html genomatrix html genotype2phase html getAlleleCounts html getAlleleQuality html getAreaFromGeneNames html getDefaultMapBiasExpMean html getSnpIdFromLocation html histplot html implodeList-old html import-bam-2 html import-bam html import-bcf html inferAlleles html inferAltAllele html inferGenotypes html initialize-ASEset html initialize-DetectedAI html initialize-GlobalAnalysis html initialize-RiskVariant html legendBarplot html locationplot html lva html lva.internal html makeMaskedFasta html mapBiasRef html minCountFilt html minFreqFilt html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-AllelicImbalance/00new/AllelicImbalance/help/minfreqFilt.html multiAllelicFilt html phase2genotype html phaseArray2phaseMatrix html phaseMatrix2Array html randomRef html reads html refAllele html regionSummary html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-AllelicImbalance/00new/AllelicImbalance/help/regionSummary.html scanForHeterozygotes-old html ** 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) Making 'packages.html' ... done
AllelicImbalance.Rcheck/tests/test-all.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 13.43 0.92 14.32
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
name | user | system | elapsed | |
ASEset-barplot | 0.16 | 0.00 | 0.15 | |
ASEset-class | 0.28 | 0.06 | 0.35 | |
ASEset-filters | 0.06 | 0.00 | 0.07 | |
ASEset-gbarplot | 0.03 | 0.00 | 0.03 | |
ASEset-glocationplot | 3.72 | 0.11 | 3.83 | |
ASEset-gviztrack | 0.55 | 0.08 | 0.62 | |
ASEset-scanForHeterozygotes | 1.98 | 0.03 | 2.02 | |
ASEset.old | 0 | 0 | 0 | |
ASEset.sim | 0 | 0 | 0 | |
ASEsetFromBam | 0.00 | 0.01 | 0.01 | |
DetectedAI-class | 0.11 | 0.00 | 0.11 | |
DetectedAI-plot | 0.92 | 0.00 | 0.92 | |
DetectedAI-summary | 0.08 | 0.00 | 0.08 | |
GRvariants | 0.00 | 0.02 | 0.02 | |
GlobalAnalysis-class | 0 | 0 | 0 | |
LinkVariantAlmlof-class | 0 | 0 | 0 | |
LinkVariantAlmlof-plot | 1.58 | 0.01 | 1.59 | |
RegionSummary-class | 0 | 0 | 0 | |
RiskVariant-class | 0 | 0 | 0 | |
annotation-wrappers | 2.78 | 0.36 | 3.14 | |
annotationBarplot | 0 | 0 | 0 | |
barplot-lattice-support | 0.08 | 0.00 | 0.08 | |
binom.test | 0.04 | 0.00 | 0.05 | |
chisq.test | 0.08 | 0.00 | 0.07 | |
cigar-utilities | 0.02 | 0.00 | 0.02 | |
countAllelesFromBam | 0 | 0 | 0 | |
coverageMatrixListFromGAL | 0.51 | 0.02 | 0.53 | |
decorateWithExons | 0 | 0 | 0 | |
decorateWithGenes | 0.02 | 0.00 | 0.02 | |
defaultMapBias | 0.05 | 0.00 | 0.04 | |
defaultPhase | 0 | 0 | 0 | |
detectAI | 0.11 | 0.00 | 0.11 | |
fractionPlotDf | 0.01 | 0.00 | 0.02 | |
gba | 0 | 0 | 0 | |
genomatrix | 0 | 0 | 0 | |
genotype2phase | 0.01 | 0.00 | 0.02 | |
getAlleleCounts | 3.08 | 0.03 | 3.11 | |
getAlleleQuality | 4.14 | 0.02 | 4.16 | |
getAreaFromGeneNames | 0.34 | 0.01 | 0.35 | |
getDefaultMapBiasExpMean | 0.03 | 0.00 | 0.03 | |
getSnpIdFromLocation | 13.70 | 2.02 | 15.72 | |
histplot | 0 | 0 | 0 | |
implodeList-old | 0 | 0 | 0 | |
import-bam-2 | 0 | 0 | 0 | |
import-bam | 21.36 | 0.42 | 21.78 | |
import-bcf | 0.97 | 0.03 | 1.00 | |
inferAlleles | 0.02 | 0.00 | 0.02 | |
inferAltAllele | 0.01 | 0.00 | 0.01 | |
inferGenotypes | 0.02 | 0.00 | 0.02 | |
initialize-ASEset | 0.09 | 0.00 | 0.09 | |
initialize-DetectedAI | 0.07 | 0.00 | 0.06 | |
initialize-GlobalAnalysis | 0 | 0 | 0 | |
initialize-RiskVariant | 0 | 0 | 0 | |
legendBarplot | 0 | 0 | 0 | |
locationplot | 0.99 | 0.02 | 1.00 | |
lva | 7.39 | 0.00 | 7.39 | |
lva.internal | 0.39 | 0.00 | 0.39 | |
makeMaskedFasta | 1.05 | 0.00 | 1.07 | |
mapBiasRef | 0.03 | 0.00 | 0.03 | |
minCountFilt | 0.07 | 0.00 | 0.07 | |
minFreqFilt | 0.08 | 0.00 | 0.08 | |
multiAllelicFilt | 0.02 | 0.00 | 0.02 | |
phase2genotype | 0.01 | 0.01 | 0.03 | |
phaseArray2phaseMatrix | 0.00 | 0.02 | 0.02 | |
phaseMatrix2Array | 0.02 | 0.00 | 0.01 | |
randomRef | 0.02 | 0.00 | 0.02 | |
reads | 0 | 0 | 0 | |
refAllele | 0.01 | 0.00 | 0.01 | |
regionSummary | 0.41 | 0.00 | 0.41 | |
scanForHeterozygotes-old | 3.62 | 0.00 | 3.62 | |