Jesper R Gadin
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/AllelicImbalance |
| Branch: master |
| Last Commit: 16a3ffe |
| Last Changed Date: 2019-04-02 07:25:49 -0400 (Tue, 02 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:08:49 -0400 (Tue, 09 Apr 2019).
| Package 42/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AllelicImbalance 1.21.2 Jesper R Gadin
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: AllelicImbalance |
| Version: 1.21.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.21.2.tar.gz |
| StartedAt: 2019-04-08 23:47:55 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:58:39 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 643.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AllelicImbalance.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.21.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.21.2’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getSnpIdFromLocation 58.147 3.555 61.795
import-bam 26.512 0.502 27.073
lva 13.461 0.040 13.501
ASEset-glocationplot 7.129 0.266 7.397
annotation-wrappers 6.096 0.555 6.653
getAlleleCounts 5.404 0.042 5.446
scanForHeterozygotes-old 5.156 0.019 5.174
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AllelicImbalance ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, 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, rowMeans, rowSums,
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 FAILED: 0
>
>
>
> proc.time()
user system elapsed
23.441 1.720 25.116
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
| name | user | system | elapsed | |
| ASEset-barplot | 0.476 | 0.018 | 0.494 | |
| ASEset-class | 0.975 | 0.068 | 1.043 | |
| ASEset-filters | 0.168 | 0.003 | 0.171 | |
| ASEset-gbarplot | 0.108 | 0.002 | 0.111 | |
| ASEset-glocationplot | 7.129 | 0.266 | 7.397 | |
| ASEset-gviztrack | 0.881 | 0.133 | 1.015 | |
| ASEset-scanForHeterozygotes | 2.650 | 0.059 | 2.708 | |
| ASEset.old | 0 | 0 | 0 | |
| ASEset.sim | 0 | 0 | 0 | |
| ASEsetFromBam | 0.003 | 0.003 | 0.006 | |
| DetectedAI-class | 0.279 | 0.004 | 0.284 | |
| DetectedAI-plot | 2.295 | 0.022 | 2.323 | |
| DetectedAI-summary | 0.234 | 0.012 | 0.244 | |
| GRvariants | 0.002 | 0.002 | 0.005 | |
| GlobalAnalysis-class | 0.002 | 0.002 | 0.005 | |
| LinkVariantAlmlof-class | 0 | 0 | 0 | |
| LinkVariantAlmlof-plot | 2.432 | 0.010 | 2.443 | |
| RegionSummary-class | 0.000 | 0.000 | 0.001 | |
| RiskVariant-class | 0 | 0 | 0 | |
| annotation-wrappers | 6.096 | 0.555 | 6.653 | |
| annotationBarplot | 0.000 | 0.001 | 0.000 | |
| barplot-lattice-support | 0.305 | 0.003 | 0.309 | |
| binom.test | 0.166 | 0.005 | 0.171 | |
| chisq.test | 0.284 | 0.004 | 0.287 | |
| cigar-utilities | 0.020 | 0.001 | 0.021 | |
| countAllelesFromBam | 0.004 | 0.005 | 0.009 | |
| coverageMatrixListFromGAL | 1.175 | 0.050 | 1.224 | |
| decorateWithExons | 0.004 | 0.004 | 0.007 | |
| decorateWithGenes | 0.003 | 0.002 | 0.005 | |
| defaultMapBias | 0.055 | 0.011 | 0.069 | |
| defaultPhase | 0.002 | 0.000 | 0.002 | |
| detectAI | 0.224 | 0.032 | 0.255 | |
| fractionPlotDf | 0.066 | 0.004 | 0.071 | |
| gba | 0.000 | 0.001 | 0.001 | |
| genomatrix | 0.000 | 0.000 | 0.001 | |
| genotype2phase | 0.046 | 0.006 | 0.052 | |
| getAlleleCounts | 5.404 | 0.042 | 5.446 | |
| getAlleleQuality | 4.954 | 0.033 | 4.987 | |
| getAreaFromGeneNames | 0.438 | 0.010 | 0.447 | |
| getDefaultMapBiasExpMean | 0.089 | 0.005 | 0.093 | |
| getSnpIdFromLocation | 58.147 | 3.555 | 61.795 | |
| histplot | 0.001 | 0.001 | 0.000 | |
| implodeList-old | 0.011 | 0.001 | 0.011 | |
| import-bam-2 | 0.011 | 0.001 | 0.011 | |
| import-bam | 26.512 | 0.502 | 27.073 | |
| import-bcf | 1.197 | 0.039 | 1.238 | |
| inferAlleles | 0.057 | 0.003 | 0.060 | |
| inferAltAllele | 0.052 | 0.002 | 0.055 | |
| inferGenotypes | 0.072 | 0.002 | 0.074 | |
| initialize-ASEset | 0.068 | 0.001 | 0.069 | |
| initialize-DetectedAI | 0.165 | 0.003 | 0.168 | |
| initialize-GlobalAnalysis | 0.005 | 0.003 | 0.008 | |
| initialize-RiskVariant | 0.002 | 0.002 | 0.005 | |
| legendBarplot | 0.000 | 0.000 | 0.001 | |
| locationplot | 3.001 | 0.076 | 3.077 | |
| lva | 13.461 | 0.040 | 13.501 | |
| lva.internal | 0.401 | 0.003 | 0.404 | |
| makeMaskedFasta | 1.183 | 0.006 | 1.189 | |
| mapBiasRef | 0.020 | 0.003 | 0.022 | |
| minCountFilt | 0.208 | 0.003 | 0.211 | |
| minFreqFilt | 0.229 | 0.004 | 0.233 | |
| multiAllelicFilt | 0.033 | 0.003 | 0.037 | |
| phase2genotype | 0.070 | 0.005 | 0.075 | |
| phaseArray2phaseMatrix | 0.010 | 0.004 | 0.014 | |
| phaseMatrix2Array | 0.009 | 0.005 | 0.014 | |
| randomRef | 0.063 | 0.004 | 0.066 | |
| reads | 0.000 | 0.000 | 0.001 | |
| refAllele | 0.023 | 0.008 | 0.031 | |
| regionSummary | 0.770 | 0.011 | 0.780 | |
| scanForHeterozygotes-old | 5.156 | 0.019 | 5.174 | |