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CHECK report for BRGenomics on tokay1

This page was generated on 2020-08-07 12:20:09 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BRGenomics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 198/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRGenomics 1.1.2
Mike DeBerardine
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BRGenomics
Branch: master
Last Commit: 932ee49
Last Changed Date: 2020-05-15 19:52:35 -0400 (Fri, 15 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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: BRGenomics
Version: 1.1.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BRGenomics_1.1.2.tar.gz
StartedAt: 2020-08-07 06:14:57 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 06:26:50 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 713.5 seconds
RetCode: 0
Status:  OK  
CheckDir: BRGenomics.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:BRGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BRGenomics_1.1.2.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BRGenomics.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 'BRGenomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BRGenomics' version '1.1.2'
* 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 whether package 'BRGenomics' 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
getDESeqResults 18.6   0.45   19.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getDESeqResults 19.99   0.09   20.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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

BRGenomics.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BRGenomics_1.1.2.tar.gz && rm -rf BRGenomics.buildbin-libdir && mkdir BRGenomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BRGenomics.buildbin-libdir BRGenomics_1.1.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BRGenomics_1.1.2.zip && rm BRGenomics_1.1.2.tar.gz BRGenomics_1.1.2.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  587k  100  587k    0     0  13.9M      0 --:--:-- --:--:-- --:--:-- 15.5M

install for i386

* installing *source* package 'BRGenomics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BRGenomics'
    finding HTML links ... done
    BRGenomics-package                      html  
    PROseq-data                             html  
    applyNFsGRanges                         html  
    binNDimensions                          html  
    bootstrap-signal-by-position            html  
    genebodies                              html  
    getCountsByPositions                    html  
    getCountsByRegions                      html  
    getDESeqDataSet                         html  
    getDESeqResults                         html  
    getMaxPositionsBySignal                 html  
    getPausingIndices                       html  
    getSpikeInCounts                        html  
    getSpikeInNFs                           html  
    getStrandedCoverage                     html  
    import-functions                        html  
    import_bam                              html  
    intersectByGene                         html  
    makeGRangesBRG                          html  
    mergeGRangesData                        html  
    mergeReplicates                         html  
    subsampleBySpikeIn                      html  
    subsampleGRanges                        html  
    subsetRegionsBySignal                   html  
    tidyChromosomes                         html  
    txs_dm6_chr4                            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 'BRGenomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BRGenomics' as BRGenomics_1.1.2.zip
* DONE (BRGenomics)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BRGenomics' successfully unpacked and MD5 sums checked

Tests output

BRGenomics.Rcheck/tests_i386/testthat.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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(BRGenomics)
Loading required package: rtracklayer
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
> 
> test_check("BRGenomics")
== testthat results  ===========================================================
[ OK: 562 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 163.60    8.60  172.62 

BRGenomics.Rcheck/tests_x64/testthat.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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(BRGenomics)
Loading required package: rtracklayer
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
> 
> test_check("BRGenomics")
== testthat results  ===========================================================
[ OK: 562 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 152.29    3.65  156.20 

Example timings

BRGenomics.Rcheck/examples_i386/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.30.00.3
binNDimensions0.680.260.95
bootstrap-signal-by-position0.670.000.67
genebodies0.310.000.31
getCountsByPositions0.860.020.88
getCountsByRegions0.200.010.21
getDESeqDataSet0.750.020.77
getDESeqResults18.60 0.4519.05
getMaxPositionsBySignal0.290.000.29
getPausingIndices1.310.011.33
getSpikeInCounts0.360.020.37
getSpikeInNFs0.570.000.56
getStrandedCoverage1.500.081.58
import-functions0.470.000.47
import_bam0.640.000.64
intersectByGene0.980.000.98
makeGRangesBRG000
mergeGRangesData1.20.11.3
mergeReplicates0.740.000.73
subsampleBySpikeIn0.720.010.73
subsampleGRanges0.130.000.13
subsetRegionsBySignal0.980.061.05
tidyChromosomes0.900.040.94

BRGenomics.Rcheck/examples_x64/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.500.020.52
binNDimensions0.750.030.78
bootstrap-signal-by-position0.860.010.88
genebodies0.330.020.34
getCountsByPositions1.960.031.98
getCountsByRegions0.310.030.35
getDESeqDataSet1.200.021.22
getDESeqResults19.99 0.0920.08
getMaxPositionsBySignal0.390.020.41
getPausingIndices0.850.000.84
getSpikeInCounts0.460.000.47
getSpikeInNFs0.660.000.66
getStrandedCoverage1.840.001.84
import-functions0.960.000.95
import_bam0.780.000.78
intersectByGene1.440.001.44
makeGRangesBRG000
mergeGRangesData1.780.001.78
mergeReplicates1.340.001.35
subsampleBySpikeIn1.280.001.28
subsampleGRanges0.090.000.10
subsetRegionsBySignal2.100.012.11
tidyChromosomes1.090.101.18