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CHECK report for consensusSeekeR on machv2

This page was generated on 2020-10-17 11:58:18 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE consensusSeekeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 365/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.16.0
Astrid Deschenes
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/consensusSeekeR
Branch: RELEASE_3_11
Last Commit: 092eafd
Last Changed Date: 2020-04-27 14:52:45 -0400 (Mon, 27 Apr 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: consensusSeekeR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings consensusSeekeR_1.16.0.tar.gz
StartedAt: 2020-10-17 00:00:28 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:05:29 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 301.6 seconds
RetCode: 0
Status:  OK 
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings consensusSeekeR_1.16.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/consensusSeekeR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘consensusSeekeR’ 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

consensusSeekeR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL consensusSeekeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘consensusSeekeR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (consensusSeekeR)

Tests output

consensusSeekeR.Rcheck/tests/runTests.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-apple-darwin17.0 (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.

> ## Run all tests present in the package
> BiocGenerics:::testPackage("consensusSeekeR")

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


Attaching package: 'S4Vectors'

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

    expand.grid



RUNIT TEST PROTOCOL -- Sat Oct 17 00:05:20 2020 
*********************************************** 
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
consensusSeekeR RUnit Tests - 56 test functions, 0 errors, 0 failures
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 21.465   0.738  22.196 

Example timings

consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.5280.0901.618
A549_CTCF_MYJ_Peaks_partial0.6850.0120.698
A549_CTCF_MYN_NarrowPeaks_partial0.6470.0110.659
A549_CTCF_MYN_Peaks_partial1.3480.0161.366
A549_FOSL2_01_NarrowPeaks_partial0.4580.0100.469
A549_FOSL2_01_Peaks_partial0.6750.0230.699
A549_FOXA1_01_NarrowPeaks_partial0.6040.0130.617
A549_FOXA1_01_Peaks_partial0.9730.0140.987
A549_NR3C1_CFQ_NarrowPeaks_partial0.5140.0110.525
A549_NR3C1_CFQ_Peaks_partial0.7290.0170.745
A549_NR3C1_CFR_NarrowPeaks_partial0.5340.0110.544
A549_NR3C1_CFR_Peaks_partial0.5780.0110.590
A549_NR3C1_CFS_NarrowPeaks_partial1.5280.0191.549
A549_NR3C1_CFS_Peaks_partial1.5240.0171.541
NOrMAL_nucleosome_positions1.0430.0221.066
NOrMAL_nucleosome_ranges1.0760.0181.094
NucPosSimulator_nucleosome_positions1.0940.0161.111
NucPosSimulator_nucleosome_ranges1.1280.0181.147
PING_nucleosome_positions0.7770.0160.794
PING_nucleosome_ranges0.6440.0190.664
findConsensusPeakRegions1.2170.0161.233
findConsensusPeakRegionsValidation0.1490.0100.159
readNarrowPeakFile0.1460.0030.149