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CHECK report for AllelicImbalance on tokay1

This page was generated on 2020-08-11 11:40:04 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AllelicImbalance PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 42/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.27.0
Jesper R Gadin
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: master
Last Commit: 053ddfb
Last Changed Date: 2020-04-27 14:36:41 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.27.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AllelicImbalance.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AllelicImbalance_1.27.0.tar.gz
StartedAt: 2020-08-11 01:15:51 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 01:27:38 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 707.5 seconds
RetCode: 0
Status:  OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AllelicImbalance.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AllelicImbalance_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AllelicImbalance.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.27.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
import-bam          19.38   0.04   23.11
lva                  9.39   0.00    9.40
annotation-wrappers  4.90   0.41    5.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
import-bam               28.23   0.37   28.62
getSnpIdFromLocation     20.47   1.00   21.92
lva                      12.67   0.01   12.71
getAlleleCounts           7.51   0.01    7.53
annotation-wrappers       7.19   0.22    7.41
scanForHeterozygotes-old  6.58   0.00    6.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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


Installation output

AllelicImbalance.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/AllelicImbalance_1.27.0.tar.gz && rm -rf AllelicImbalance.buildbin-libdir && mkdir AllelicImbalance.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.27.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AllelicImbalance_1.27.0.zip && rm AllelicImbalance_1.27.0.tar.gz AllelicImbalance_1.27.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  570k  100  570k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 12.3M

install for i386

* 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  
    multiAllelicFilt                        html  
    phase2genotype                          html  
    phaseArray2phaseMatrix                  html  
    phaseMatrix2Array                       html  
    randomRef                               html  
    reads                                   html  
    refAllele                               html  
    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

install for x64

* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.27.0.zip
* DONE (AllelicImbalance)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AllelicImbalance' successfully unpacked and MD5 sums checked

Tests output

AllelicImbalance.Rcheck/tests_i386/test-all.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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: 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: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


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 
  21.23    2.15   23.37 

AllelicImbalance.Rcheck/tests_x64/test-all.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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
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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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: 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: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


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 
  18.15    0.76   18.95 

Example timings

AllelicImbalance.Rcheck/examples_i386/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.310.210.51
ASEset-class0.810.140.96
ASEset-filters0.080.000.08
ASEset-gbarplot0.050.010.06
ASEset-glocationplot4.650.184.83
ASEset-gviztrack0.850.030.88
ASEset-scanForHeterozygotes2.030.072.11
ASEset.old000
ASEset.sim000
ASEsetFromBam000
DetectedAI-class0.090.020.11
DetectedAI-plot1.220.031.25
DetectedAI-summary0.110.000.11
GRvariants000
GlobalAnalysis-class000
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot2.320.062.39
RegionSummary-class000
RiskVariant-class000
annotation-wrappers4.900.415.33
annotationBarplot000
barplot-lattice-support0.120.020.14
binom.test0.070.000.06
chisq.test0.140.000.14
cigar-utilities0.010.000.01
countAllelesFromBam000
coverageMatrixListFromGAL0.780.200.99
decorateWithExons0.020.000.01
decorateWithGenes0.010.000.02
defaultMapBias0.020.050.06
defaultPhase000
detectAI0.060.120.19
fractionPlotDf0.030.050.08
gba000
genomatrix000
genotype2phase0.070.010.08
getAlleleCounts3.970.244.20
getAlleleQuality3.730.033.77
getAreaFromGeneNames0.360.010.37
getDefaultMapBiasExpMean0.050.000.05
getSnpIdFromLocation000
histplot000
implodeList-old0.010.000.01
import-bam-2000
import-bam19.38 0.0423.11
import-bcf0.890.010.91
inferAlleles0.000.020.01
inferAltAllele0.030.000.04
inferGenotypes0.030.000.03
initialize-ASEset0.080.000.07
initialize-DetectedAI0.090.000.10
initialize-GlobalAnalysis000
initialize-RiskVariant0.020.000.01
legendBarplot000
locationplot1.390.001.39
lva9.390.009.40
lva.internal0.340.000.34
makeMaskedFasta0.920.000.92
mapBiasRef0.020.000.02
minCountFilt0.080.000.07
minFreqFilt0.080.010.10
multiAllelicFilt0.010.000.01
phase2genotype0.050.000.05
phaseArray2phaseMatrix0.010.000.02
phaseMatrix2Array0.020.000.01
randomRef0.020.000.02
reads000
refAllele0.010.020.03
regionSummary0.590.010.61
scanForHeterozygotes-old4.770.004.76

AllelicImbalance.Rcheck/examples_x64/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.270.000.26
ASEset-class1.410.001.40
ASEset-filters0.060.000.06
ASEset-gbarplot0.050.010.06
ASEset-glocationplot4.920.054.97
ASEset-gviztrack0.720.050.77
ASEset-scanForHeterozygotes3.030.043.08
ASEset.old000
ASEset.sim000
ASEsetFromBam0.010.000.01
DetectedAI-class0.180.000.17
DetectedAI-plot1.530.001.53
DetectedAI-summary0.220.010.24
GRvariants000
GlobalAnalysis-class0.010.020.03
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot2.950.022.97
RegionSummary-class000
RiskVariant-class000
annotation-wrappers7.190.227.41
annotationBarplot000
barplot-lattice-support0.140.000.14
binom.test0.060.000.06
chisq.test0.150.000.14
cigar-utilities0.010.000.02
countAllelesFromBam000
coverageMatrixListFromGAL0.950.000.95
decorateWithExons0.000.020.02
decorateWithGenes000
defaultMapBias0.040.010.04
defaultPhase000
detectAI0.100.000.11
fractionPlotDf0.050.000.05
gba000
genomatrix000
genotype2phase0.020.020.03
getAlleleCounts7.510.017.53
getAlleleQuality4.130.034.17
getAreaFromGeneNames0.330.020.35
getDefaultMapBiasExpMean0.070.020.09
getSnpIdFromLocation20.47 1.0021.92
histplot000
implodeList-old000
import-bam-2000
import-bam28.23 0.3728.62
import-bcf1.520.001.52
inferAlleles0.010.020.03
inferAltAllele0.040.010.05
inferGenotypes0.060.020.07
initialize-ASEset0.150.000.16
initialize-DetectedAI0.190.000.19
initialize-GlobalAnalysis0.020.000.01
initialize-RiskVariant0.000.010.02
legendBarplot000
locationplot2.360.022.37
lva12.67 0.0112.71
lva.internal0.370.020.39
makeMaskedFasta1.440.001.44
mapBiasRef0.030.000.03
minCountFilt0.130.000.12
minFreqFilt0.120.020.14
multiAllelicFilt0.030.000.03
phase2genotype0.050.030.08
phaseArray2phaseMatrix0.020.010.03
phaseMatrix2Array0.010.000.02
randomRef0.030.020.05
reads000
refAllele0.030.010.04
regionSummary1.100.001.11
scanForHeterozygotes-old6.580.006.61