Back to Multiple platform build/check report for BioC 3.11
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BRGenomics on tokay2

This page was generated on 2020-10-17 11:56:11 -0400 (Sat, 17 Oct 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 203/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRGenomics 1.0.3
Mike DeBerardine
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BRGenomics
Branch: RELEASE_3_11
Last Commit: 50f2560
Last Changed Date: 2020-08-28 13:05:31 -0400 (Fri, 28 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BRGenomics
Version: 1.0.3
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BRGenomics_1.0.3.tar.gz
StartedAt: 2020-10-17 02:06:46 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:18:17 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 690.6 seconds
RetCode: 0
Status:  OK  
CheckDir: BRGenomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BRGenomics_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BRGenomics.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.0.3'
* 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 13.2   0.32   13.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getDESeqResults 13.15   0.11   13.25
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/BRGenomics_1.0.3.tar.gz && rm -rf BRGenomics.buildbin-libdir && mkdir BRGenomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BRGenomics.buildbin-libdir BRGenomics_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BRGenomics_1.0.3.zip && rm BRGenomics_1.0.3.tar.gz BRGenomics_1.0.3.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  9230k      0 --:--:-- --:--:-- --:--:-- 10.0M

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_1.0.3.zip
* DONE (BRGenomics)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BRGenomics' successfully unpacked and MD5 sums checked

Tests output

BRGenomics.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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, 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 
 139.35    5.76  146.15 

BRGenomics.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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, 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 
 141.01    4.79  167.00 

Example timings

BRGenomics.Rcheck/examples_i386/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.340.160.50
binNDimensions0.430.190.61
bootstrap-signal-by-position0.360.030.39
genebodies0.160.010.17
getCountsByPositions0.420.020.44
getCountsByRegions0.170.000.17
getDESeqDataSet0.510.080.60
getDESeqResults13.20 0.3213.53
getMaxPositionsBySignal0.330.000.33
getPausingIndices1.270.041.29
getSpikeInCounts0.230.000.24
getSpikeInNFs0.420.000.42
getStrandedCoverage1.000.061.06
import-functions0.430.030.46
import_bam0.640.000.64
intersectByGene0.980.000.98
makeGRangesBRG0.020.000.02
mergeGRangesData1.810.031.84
mergeReplicates0.890.081.00
subsampleBySpikeIn0.690.000.69
subsampleGRanges0.090.000.09
subsetRegionsBySignal0.640.010.66
tidyChromosomes0.580.080.66

BRGenomics.Rcheck/examples_x64/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.370.000.37
binNDimensions0.750.060.81
bootstrap-signal-by-position1.410.011.42
genebodies0.190.000.19
getCountsByPositions0.460.050.51
getCountsByRegions0.180.020.19
getDESeqDataSet0.820.000.83
getDESeqResults13.15 0.1113.25
getMaxPositionsBySignal0.280.010.29
getPausingIndices0.660.000.66
getSpikeInCounts0.280.000.28
getSpikeInNFs0.480.000.48
getStrandedCoverage1.080.021.10
import-functions0.420.010.44
import_bam0.600.000.59
intersectByGene0.980.000.98
makeGRangesBRG000
mergeGRangesData1.110.001.11
mergeReplicates0.640.000.64
subsampleBySpikeIn0.560.000.57
subsampleGRanges0.070.000.06
subsetRegionsBySignal1.180.001.19
tidyChromosomes0.720.020.73