Jesper R Gadin
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/AllelicImbalance |
| Branch: RELEASE_3_10 |
| Last Commit: 068ad8b |
| Last Changed Date: 2019-10-29 13:08:48 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:08:06 -0400 (Wed, 15 Apr 2020).
| Package 43/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AllelicImbalance 1.24.0 Jesper R Gadin
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: AllelicImbalance |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings AllelicImbalance_1.24.0.tar.gz |
| StartedAt: 2020-04-15 01:52:28 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:00:52 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 504.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AllelicImbalance.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings AllelicImbalance_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.24.0’
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'RiskVariant-class':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 27.644 1.328 30.770
import-bam 23.404 0.144 24.470
lva 15.740 0.000 15.915
scanForHeterozygotes-old 6.988 0.004 7.059
getAlleleCounts 6.440 0.004 6.501
annotation-wrappers 6.268 0.140 6.615
ASEset-glocationplot 6.232 0.068 6.463
getAlleleQuality 5.668 0.000 5.722
* 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: 1 WARNING
See
‘/home/biocbuild/bbs-3.10-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.
AllelicImbalance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL AllelicImbalance ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
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, 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:base':
strsplit
Loading required package: Rsamtools
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
>
>
> proc.time()
user system elapsed
23.384 0.536 24.094
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
| name | user | system | elapsed | |
| ASEset-barplot | 0.684 | 0.008 | 0.695 | |
| ASEset-class | 1.472 | 0.044 | 1.522 | |
| ASEset-filters | 0.212 | 0.000 | 0.212 | |
| ASEset-gbarplot | 0.164 | 0.000 | 0.172 | |
| ASEset-glocationplot | 6.232 | 0.068 | 6.463 | |
| ASEset-gviztrack | 0.848 | 0.000 | 0.852 | |
| ASEset-scanForHeterozygotes | 2.884 | 0.004 | 2.916 | |
| ASEset.old | 0 | 0 | 0 | |
| ASEset.sim | 0 | 0 | 0 | |
| ASEsetFromBam | 0.000 | 0.004 | 0.001 | |
| DetectedAI-class | 0.36 | 0.00 | 0.37 | |
| DetectedAI-plot | 2.784 | 0.004 | 2.801 | |
| DetectedAI-summary | 0.316 | 0.008 | 0.327 | |
| GRvariants | 0.000 | 0.000 | 0.001 | |
| GlobalAnalysis-class | 0.000 | 0.000 | 0.001 | |
| LinkVariantAlmlof-class | 0.004 | 0.000 | 0.000 | |
| LinkVariantAlmlof-plot | 3.776 | 0.000 | 3.797 | |
| RegionSummary-class | 0 | 0 | 0 | |
| RiskVariant-class | 0 | 0 | 0 | |
| annotation-wrappers | 6.268 | 0.140 | 6.615 | |
| annotationBarplot | 0 | 0 | 0 | |
| barplot-lattice-support | 0.312 | 0.000 | 0.314 | |
| binom.test | 0.288 | 0.000 | 0.290 | |
| chisq.test | 0.540 | 0.000 | 0.543 | |
| cigar-utilities | 0.020 | 0.000 | 0.018 | |
| countAllelesFromBam | 0.000 | 0.000 | 0.002 | |
| coverageMatrixListFromGAL | 2.396 | 0.000 | 2.418 | |
| decorateWithExons | 0.000 | 0.000 | 0.002 | |
| decorateWithGenes | 0.004 | 0.000 | 0.002 | |
| defaultMapBias | 0.048 | 0.004 | 0.070 | |
| defaultPhase | 0.000 | 0.000 | 0.001 | |
| detectAI | 0.372 | 0.000 | 0.401 | |
| fractionPlotDf | 0.092 | 0.004 | 0.097 | |
| gba | 0 | 0 | 0 | |
| genomatrix | 0.000 | 0.000 | 0.001 | |
| genotype2phase | 0.036 | 0.004 | 0.041 | |
| getAlleleCounts | 6.440 | 0.004 | 6.501 | |
| getAlleleQuality | 5.668 | 0.000 | 5.722 | |
| getAreaFromGeneNames | 0.468 | 0.000 | 0.470 | |
| getDefaultMapBiasExpMean | 0.100 | 0.000 | 0.103 | |
| getSnpIdFromLocation | 27.644 | 1.328 | 30.770 | |
| histplot | 0 | 0 | 0 | |
| implodeList-old | 0.012 | 0.000 | 0.010 | |
| import-bam-2 | 0.012 | 0.000 | 0.013 | |
| import-bam | 23.404 | 0.144 | 24.470 | |
| import-bcf | 1.224 | 0.016 | 1.295 | |
| inferAlleles | 0.076 | 0.004 | 0.078 | |
| inferAltAllele | 0.088 | 0.000 | 0.088 | |
| inferGenotypes | 0.172 | 0.000 | 0.175 | |
| initialize-ASEset | 0.104 | 0.000 | 0.104 | |
| initialize-DetectedAI | 0.364 | 0.000 | 0.365 | |
| initialize-GlobalAnalysis | 0.004 | 0.000 | 0.005 | |
| initialize-RiskVariant | 0.004 | 0.000 | 0.002 | |
| legendBarplot | 0 | 0 | 0 | |
| locationplot | 2.992 | 0.004 | 2.999 | |
| lva | 15.740 | 0.000 | 15.915 | |
| lva.internal | 0.668 | 0.004 | 0.696 | |
| makeMaskedFasta | 1.152 | 0.004 | 1.160 | |
| mapBiasRef | 0.040 | 0.000 | 0.041 | |
| minCountFilt | 0.324 | 0.000 | 0.327 | |
| minFreqFilt | 0.332 | 0.000 | 0.331 | |
| multiAllelicFilt | 0.080 | 0.000 | 0.081 | |
| phase2genotype | 0.100 | 0.000 | 0.101 | |
| phaseArray2phaseMatrix | 0.008 | 0.000 | 0.009 | |
| phaseMatrix2Array | 0.008 | 0.000 | 0.007 | |
| randomRef | 0.064 | 0.000 | 0.064 | |
| reads | 0 | 0 | 0 | |
| refAllele | 0.016 | 0.004 | 0.024 | |
| regionSummary | 0.904 | 0.012 | 0.931 | |
| scanForHeterozygotes-old | 6.988 | 0.004 | 7.059 | |