Jesper R Gadin
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/AllelicImbalance |
| git_branch: master |
| git_last_commit: 7e81c3a |
| git_last_commit_date: 2021-11-17 15:17:12 -0400 (Wed, 17 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
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 |
##############################################################################
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###
### 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
##############################################################################
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###
### 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 | |