BioC 3.4: CHECK report for consensusSeekeR on malbec1

Package: consensusSeekeR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.2.0.tar.gz

StartedAt: 2017-04-14 21:46:42 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:49:47 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 185.2 seconds

RetCode: 0

Status:  OK

CheckDir: consensusSeekeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/consensusSeekeR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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 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 ... 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
  ‘/home/biocbuild/bbs-3.4-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	0.992	0.016	1.010
A549_CTCF_MYJ_Peaks_partial	0.316	0.004	0.317
A549_CTCF_MYN_NarrowPeaks_partial	0.392	0.000	0.392
A549_CTCF_MYN_Peaks_partial	0.536	0.004	0.540
A549_FOSL2_01_NarrowPeaks_partial	0.276	0.004	0.280
A549_FOSL2_01_Peaks_partial	0.340	0.000	0.342
A549_FOXA1_01_NarrowPeaks_partial	0.340	0.000	0.339
A549_FOXA1_01_Peaks_partial	0.512	0.000	0.510
A549_NR3C1_CFQ_NarrowPeaks_partial	0.28	0.00	0.28
A549_NR3C1_CFQ_Peaks_partial	0.404	0.000	0.402
A549_NR3C1_CFR_NarrowPeaks_partial	0.280	0.000	0.281
A549_NR3C1_CFR_Peaks_partial	0.268	0.000	0.266
A549_NR3C1_CFS_NarrowPeaks_partial	0.884	0.004	0.888
A549_NR3C1_CFS_Peaks_partial	0.992	0.000	0.994
NOrMAL_nucleosome_positions	0.616	0.008	0.621
NOrMAL_nucleosome_ranges	0.684	0.000	0.684
NucPosSimulator_nucleosome_positions	0.600	0.000	0.602
NucPosSimulator_nucleosome_ranges	0.644	0.008	0.657
PING_nucleosome_positions	0.488	0.008	0.497
PING_nucleosome_ranges	0.416	0.004	0.422
findConsensusPeakRegions	0.780	0.008	0.786
findConsensusPeakRegionsValidation	0.032	0.000	0.033
readNarrowPeakFile	0.064	0.000	0.063