BioC 3.3: CHECK report for consensusSeekeR on morelia

Package: consensusSeekeR

Version: 0.99.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings consensusSeekeR_0.99.6.tar.gz

StartedAt: 2016-04-21 00:55:02 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:58:16 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 194.4 seconds

RetCode: 0

Status:  OK

CheckDir: consensusSeekeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings consensusSeekeR_0.99.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/consensusSeekeR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘0.99.6’
* 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 ... [14s/15s] 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 loading without being on the library search path ... 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 ... [21s/23s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [27s/27s]
 [27s/28s] 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	0.893	0.015	0.918
A549_CTCF_MYJ_Peaks_partial	0.440	0.014	0.455
A549_CTCF_MYN_NarrowPeaks_partial	0.710	0.012	0.722
A549_CTCF_MYN_Peaks_partial	0.639	0.036	0.677
A549_FOSL2_01_NarrowPeaks_partial	0.333	0.013	0.346
A549_FOSL2_01_Peaks_partial	0.478	0.010	0.488
A549_FOXA1_01_NarrowPeaks_partial	0.513	0.014	0.527
A549_FOXA1_01_Peaks_partial	0.642	0.010	0.653
A549_NR3C1_CFQ_NarrowPeaks_partial	0.390	0.013	0.403
A549_NR3C1_CFQ_Peaks_partial	0.499	0.016	0.772
A549_NR3C1_CFR_NarrowPeaks_partial	0.387	0.012	0.399
A549_NR3C1_CFR_Peaks_partial	0.378	0.013	0.435
A549_NR3C1_CFS_NarrowPeaks_partial	1.073	0.015	1.088
A549_NR3C1_CFS_Peaks_partial	1.033	0.016	1.050
NOrMAL_nucleosome_positions	0.687	0.017	0.708
NOrMAL_nucleosome_ranges	0.925	0.014	0.938
NucPosSimulator_nucleosome_positions	0.694	0.018	0.712
NucPosSimulator_nucleosome_ranges	0.791	0.018	0.809
PING_nucleosome_positions	0.566	0.017	0.584
PING_nucleosome_ranges	0.458	0.017	0.476
findConsensusPeakRegions	0.981	0.010	0.992
findConsensusPeakRegionsValidation	0.053	0.009	0.062
readNarrowPeakFile	0.091	0.002	0.092