BioC 3.5: CHECK report for consensusSeekeR on oaxaca

Package: consensusSeekeR

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.3.0.tar.gz

StartedAt: 2017-03-04 01:08:49 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:12:25 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 215.9 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/consensusSeekeR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.3.0’
* 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 ... NOTE
findConsensusPeakRegionsValidation: no visible global function
  definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/consensusSeekeR.Rcheck/00check.log’
for details.

* 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	1.577	0.045	1.622
A549_CTCF_MYJ_Peaks_partial	0.740	0.023	0.763
A549_CTCF_MYN_NarrowPeaks_partial	0.356	0.018	0.375
A549_CTCF_MYN_Peaks_partial	0.534	0.023	0.557
A549_FOSL2_01_NarrowPeaks_partial	0.375	0.021	0.396
A549_FOSL2_01_Peaks_partial	0.380	0.016	0.396
A549_FOXA1_01_NarrowPeaks_partial	0.448	0.020	0.468
A549_FOXA1_01_Peaks_partial	0.705	0.020	0.727
A549_NR3C1_CFQ_NarrowPeaks_partial	0.379	0.022	0.401
A549_NR3C1_CFQ_Peaks_partial	0.430	0.025	0.456
A549_NR3C1_CFR_NarrowPeaks_partial	0.316	0.015	0.332
A549_NR3C1_CFR_Peaks_partial	0.375	0.020	0.395
A549_NR3C1_CFS_NarrowPeaks_partial	1.003	0.019	1.020
A549_NR3C1_CFS_Peaks_partial	0.937	0.023	0.960
NOrMAL_nucleosome_positions	0.614	0.025	0.640
NOrMAL_nucleosome_ranges	0.891	0.024	0.915
NucPosSimulator_nucleosome_positions	0.592	0.044	0.636
NucPosSimulator_nucleosome_ranges	0.682	0.022	0.706
PING_nucleosome_positions	0.363	0.017	0.381
PING_nucleosome_ranges	0.340	0.017	0.357
findConsensusPeakRegions	0.709	0.015	0.723
findConsensusPeakRegionsValidation	0.034	0.009	0.043
readNarrowPeakFile	0.140	0.001	0.141