Jesper R Gadin
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/AllelicImbalance |
| Branch: RELEASE_3_7 |
| Last Commit: 6d6eed7 |
| Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:25:33 -0400 (Wed, 17 Oct 2018).
| Package 36/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AllelicImbalance 1.18.0 Jesper R Gadin
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: AllelicImbalance |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings AllelicImbalance_1.18.0.tar.gz |
| StartedAt: 2018-10-15 22:22:55 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 22:28:28 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 332.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AllelicImbalance.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings AllelicImbalance_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.18.0’
* 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 ... NOTE
Failed with error: 'package 'DelayedArray' could not be loaded'
Error in .requirePackage(package) :
unable to find required package 'AllelicImbalance'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* 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 18.120 0.912 19.086
import-bam 18.576 0.124 19.126
annotation-wrappers 9.920 0.148 10.076
lva 7.104 0.004 7.120
* 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 NOTE
See
‘/home/biocbuild/bbs-3.7-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.
AllelicImbalance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL AllelicImbalance ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘AllelicImbalance’ ... ** 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 * DONE (AllelicImbalance)
AllelicImbalance.Rcheck/tests/test-all.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, 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
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
13.020 0.364 13.396
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
| name | user | system | elapsed | |
| ASEset-barplot | 0.272 | 0.020 | 0.294 | |
| ASEset-class | 0.408 | 0.000 | 0.407 | |
| ASEset-filters | 0.072 | 0.004 | 0.077 | |
| ASEset-gbarplot | 0.060 | 0.008 | 0.067 | |
| ASEset-glocationplot | 3.544 | 0.012 | 3.557 | |
| ASEset-gviztrack | 0.512 | 0.008 | 0.521 | |
| ASEset-scanForHeterozygotes | 1.648 | 0.000 | 1.649 | |
| ASEset.old | 0 | 0 | 0 | |
| ASEset.sim | 0.000 | 0.000 | 0.001 | |
| ASEsetFromBam | 0.000 | 0.000 | 0.001 | |
| DetectedAI-class | 0.132 | 0.000 | 0.133 | |
| DetectedAI-plot | 1.432 | 0.000 | 1.435 | |
| DetectedAI-summary | 0.164 | 0.004 | 0.168 | |
| GRvariants | 0.000 | 0.000 | 0.002 | |
| GlobalAnalysis-class | 0.004 | 0.000 | 0.002 | |
| LinkVariantAlmlof-class | 0.000 | 0.000 | 0.001 | |
| LinkVariantAlmlof-plot | 1.736 | 0.000 | 1.741 | |
| RegionSummary-class | 0 | 0 | 0 | |
| RiskVariant-class | 0.000 | 0.000 | 0.001 | |
| annotation-wrappers | 9.920 | 0.148 | 10.076 | |
| annotationBarplot | 0.000 | 0.000 | 0.001 | |
| barplot-lattice-support | 0.152 | 0.000 | 0.154 | |
| binom.test | 0.076 | 0.000 | 0.076 | |
| chisq.test | 0.156 | 0.000 | 0.158 | |
| cigar-utilities | 0.008 | 0.000 | 0.010 | |
| countAllelesFromBam | 0.004 | 0.000 | 0.001 | |
| coverageMatrixListFromGAL | 1.536 | 0.088 | 1.624 | |
| decorateWithExons | 0.000 | 0.000 | 0.002 | |
| decorateWithGenes | 0.000 | 0.004 | 0.001 | |
| defaultMapBias | 0.088 | 0.000 | 0.106 | |
| defaultPhase | 0.004 | 0.000 | 0.002 | |
| detectAI | 0.112 | 0.004 | 0.118 | |
| fractionPlotDf | 0.040 | 0.000 | 0.038 | |
| gba | 0.000 | 0.000 | 0.001 | |
| genomatrix | 0.000 | 0.000 | 0.001 | |
| genotype2phase | 0.020 | 0.000 | 0.023 | |
| getAlleleCounts | 3.396 | 0.008 | 3.412 | |
| getAlleleQuality | 3.312 | 0.000 | 3.319 | |
| getAreaFromGeneNames | 0.232 | 0.004 | 0.236 | |
| getDefaultMapBiasExpMean | 0.036 | 0.004 | 0.040 | |
| getSnpIdFromLocation | 18.120 | 0.912 | 19.086 | |
| histplot | 0 | 0 | 0 | |
| implodeList-old | 0.004 | 0.000 | 0.006 | |
| import-bam-2 | 0.008 | 0.000 | 0.007 | |
| import-bam | 18.576 | 0.124 | 19.126 | |
| import-bcf | 0.880 | 0.000 | 0.894 | |
| inferAlleles | 0.024 | 0.000 | 0.025 | |
| inferAltAllele | 0.032 | 0.000 | 0.029 | |
| inferGenotypes | 0.052 | 0.004 | 0.056 | |
| initialize-ASEset | 0.056 | 0.000 | 0.057 | |
| initialize-DetectedAI | 0.116 | 0.000 | 0.117 | |
| initialize-GlobalAnalysis | 0.000 | 0.004 | 0.003 | |
| initialize-RiskVariant | 0.000 | 0.000 | 0.001 | |
| legendBarplot | 0.000 | 0.000 | 0.001 | |
| locationplot | 1.428 | 0.008 | 1.438 | |
| lva | 7.104 | 0.004 | 7.120 | |
| lva.internal | 0.296 | 0.004 | 0.298 | |
| makeMaskedFasta | 0.868 | 0.000 | 0.869 | |
| mapBiasRef | 0.016 | 0.000 | 0.015 | |
| minCountFilt | 0.104 | 0.000 | 0.105 | |
| minFreqFilt | 0.104 | 0.000 | 0.104 | |
| multiAllelicFilt | 0.028 | 0.000 | 0.025 | |
| phase2genotype | 0.032 | 0.000 | 0.031 | |
| phaseArray2phaseMatrix | 0.004 | 0.000 | 0.006 | |
| phaseMatrix2Array | 0.004 | 0.000 | 0.005 | |
| randomRef | 0.032 | 0.000 | 0.031 | |
| reads | 0.000 | 0.000 | 0.001 | |
| refAllele | 0.012 | 0.000 | 0.013 | |
| regionSummary | 0.504 | 0.000 | 0.504 | |
| scanForHeterozygotes-old | 4.208 | 0.000 | 4.214 | |