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This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).

CHECK results for BRGenomics on tokay2

To the developers/maintainers of the BRGenomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BRGenomics.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.

raw results

Package 213/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRGenomics 1.4.0  (landing page)
Mike DeBerardine
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/BRGenomics
git_branch: RELEASE_3_13
git_last_commit: b006074
git_last_commit_date: 2021-05-19 12:50:47 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BRGenomics
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BRGenomics_1.4.0.tar.gz
StartedAt: 2021-10-14 20:27:18 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:39:24 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 725.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BRGenomics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRGenomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BRGenomics_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BRGenomics.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.0'
* 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 '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 ... WARNING
Missing link or links in documentation object 'getCountsByRegions.Rd':
  '[rtracklayer:export]{rtracklayer::import.bw}'

Missing link or links in documentation object 'import-functions.Rd':
  '[rtracklayer:export]{rtracklayer::import}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 19.67    0.5   20.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
getDESeqResults   24   0.01   24.02
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BRGenomics.Rcheck/00check.log'
for details.

Installation output

BRGenomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BRGenomics_1.4.0.tar.gz && rm -rf BRGenomics.buildbin-libdir && mkdir BRGenomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BRGenomics.buildbin-libdir BRGenomics_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BRGenomics_1.4.0.zip && rm BRGenomics_1.4.0.tar.gz BRGenomics_1.4.0.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  588k  100  588k    0     0  1406k      0 --:--:-- --:--:-- --:--:-- 1408k

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_1.4.0.zip
* DONE (BRGenomics)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BRGenomics' successfully unpacked and MD5 sums checked

Tests output

BRGenomics.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 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
> 
> test_check("BRGenomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 562 ]
> 
> proc.time()
   user  system elapsed 
 161.51    5.93  167.45

BRGenomics.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> 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 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
> 
> test_check("BRGenomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 562 ]
> 
> proc.time()
   user  system elapsed 
 181.56    4.07  186.43

Example timings

BRGenomics.Rcheck/examples_i386/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.310.030.34
binNDimensions0.450.060.51
bootstrap-signal-by-position0.390.010.40
genebodies0.260.000.27
getCountsByPositions0.520.000.51
getCountsByRegions0.250.040.28
getDESeqDataSet0.770.010.79
getDESeqResults19.67 0.5020.17
getMaxPositionsBySignal0.330.020.34
getPausingIndices0.640.030.67
getSpikeInCounts0.370.000.38
getSpikeInNFs0.70.00.7
getStrandedCoverage2.320.012.33
import-functions0.530.020.55
import_bam0.980.011.01
intersectByGene1.360.001.36
makeGRangesBRG000
mergeGRangesData1.600.041.63
mergeReplicates0.870.000.88
subsampleBySpikeIn1.110.001.11
subsampleGRanges0.110.020.12
subsetRegionsBySignal0.780.010.80
tidyChromosomes0.670.030.70

BRGenomics.Rcheck/examples_x64/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.450.000.45
binNDimensions0.520.090.61
bootstrap-signal-by-position0.490.000.48
genebodies0.260.000.27
getCountsByPositions0.60.00.6
getCountsByRegions0.250.030.28
getDESeqDataSet0.930.020.95
getDESeqResults24.00 0.0124.02
getMaxPositionsBySignal0.640.020.65
getPausingIndices0.940.010.96
getSpikeInCounts0.640.000.64
getSpikeInNFs0.830.000.82
getStrandedCoverage1.420.041.46
import-functions0.940.040.98
import_bam0.950.000.95
intersectByGene1.570.001.57
makeGRangesBRG000
mergeGRangesData1.730.001.73
mergeReplicates1.000.021.02
subsampleBySpikeIn1.170.001.17
subsampleGRanges0.140.000.14
subsetRegionsBySignal1.350.061.41
tidyChromosomes0.750.030.78