Package: consensusSeekeR

Version: 1.10.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings consensusSeekeR_1.10.0.tar.gz

StartedAt: 2019-04-15 23:08:53 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:12:09 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 196.1 seconds

RetCode: 0

Status:  OK

CheckDir: consensusSeekeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings consensusSeekeR_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/consensusSeekeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.10.0’
* 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

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL consensusSeekeR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘consensusSeekeR’ ...
** 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
* DONE (consensusSeekeR)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 -- Mon Apr 15 23:12:06 2019 
*********************************************** 
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 
 13.116   0.316  13.462 

name	user	system	elapsed
A549_CTCF_MYJ_NarrowPeaks_partial	0.948	0.044	0.992
A549_CTCF_MYJ_Peaks_partial	0.428	0.008	0.436
A549_CTCF_MYN_NarrowPeaks_partial	0.360	0.004	0.366
A549_CTCF_MYN_Peaks_partial	0.440	0.004	0.443
A549_FOSL2_01_NarrowPeaks_partial	0.788	0.000	0.790
A549_FOSL2_01_Peaks_partial	0.376	0.004	0.380
A549_FOXA1_01_NarrowPeaks_partial	0.320	0.004	0.321
A549_FOXA1_01_Peaks_partial	0.372	0.008	0.381
A549_NR3C1_CFQ_NarrowPeaks_partial	0.276	0.008	0.285
A549_NR3C1_CFQ_Peaks_partial	0.436	0.004	0.441
A549_NR3C1_CFR_NarrowPeaks_partial	0.376	0.000	0.377
A549_NR3C1_CFR_Peaks_partial	0.36	0.00	0.36
A549_NR3C1_CFS_NarrowPeaks_partial	1.104	0.004	1.111
A549_NR3C1_CFS_Peaks_partial	0.744	0.008	0.751
NOrMAL_nucleosome_positions	0.624	0.008	0.632
NOrMAL_nucleosome_ranges	0.456	0.004	0.462
NucPosSimulator_nucleosome_positions	0.484	0.008	0.495
NucPosSimulator_nucleosome_ranges	0.572	0.004	0.577
PING_nucleosome_positions	0.344	0.004	0.349
PING_nucleosome_ranges	0.268	0.004	0.272
findConsensusPeakRegions	0.460	0.000	0.458
findConsensusPeakRegionsValidation	0.040	0.000	0.041
readNarrowPeakFile	0.064	0.000	0.078