BioC 3.5: CHECK report for consensusSeekeR on veracruz2

Package: consensusSeekeR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.4.0.tar.gz

StartedAt: 2017-08-16 01:22:33 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:26:21 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 228.1 seconds

RetCode: 0

Status:  OK

CheckDir: consensusSeekeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/consensusSeekeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.4.0’
* 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 installed files from ‘inst/doc’ ... 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

* installing *source* package ‘consensusSeekeR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (consensusSeekeR)

name	user	system	elapsed
A549_CTCF_MYJ_NarrowPeaks_partial	1.770	0.035	1.823
A549_CTCF_MYJ_Peaks_partial	0.790	0.009	0.803
A549_CTCF_MYN_NarrowPeaks_partial	0.358	0.006	0.365
A549_CTCF_MYN_Peaks_partial	0.492	0.008	0.506
A549_FOSL2_01_NarrowPeaks_partial	0.267	0.007	0.276
A549_FOSL2_01_Peaks_partial	0.430	0.008	0.444
A549_FOXA1_01_NarrowPeaks_partial	0.400	0.007	0.415
A549_FOXA1_01_Peaks_partial	0.637	0.009	0.649
A549_NR3C1_CFQ_NarrowPeaks_partial	0.327	0.007	0.335
A549_NR3C1_CFQ_Peaks_partial	0.448	0.009	0.462
A549_NR3C1_CFR_NarrowPeaks_partial	0.329	0.007	0.339
A549_NR3C1_CFR_Peaks_partial	0.337	0.006	0.345
A549_NR3C1_CFS_NarrowPeaks_partial	1.000	0.010	1.019
A549_NR3C1_CFS_Peaks_partial	1.086	0.009	1.104
NOrMAL_nucleosome_positions	0.967	0.012	0.988
NOrMAL_nucleosome_ranges	0.707	0.044	0.758
NucPosSimulator_nucleosome_positions	0.676	0.012	0.695
NucPosSimulator_nucleosome_ranges	0.759	0.020	0.786
PING_nucleosome_positions	0.406	0.013	0.420
PING_nucleosome_ranges	0.362	0.009	0.373
findConsensusPeakRegions	0.949	0.010	0.968
findConsensusPeakRegionsValidation	0.047	0.006	0.053
readNarrowPeakFile	0.158	0.001	0.160