Jesper R Gadin
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/AllelicImbalance |
| Branch: RELEASE_3_9 |
| Last Commit: 04692e3 |
| Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
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 |
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### Running command:
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### /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
###
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* 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 | |