BioC 3.4: CHECK report for ChIPsim on morelia

Package: ChIPsim

Version: 1.27.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPsim_1.27.0.tar.gz

StartedAt: 2016-09-20 04:26:38 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:29:23 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 164.8 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPsim.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 ChIPsim_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ChIPsim.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPsim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPsim’ version ‘1.27.0’
* 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 ‘ChIPsim’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’
A package should be listed in only one of these fields.
* 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
print.SimulatedFeature: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/ChIPsim.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ChIPsim-package	0	0	0
bindDens2readDens	1.618	0.070	1.688
decodeQuality	0.002	0.000	0.002
defaultControl	0.003	0.001	0.003
defaultErrorProb	0.001	0.000	0.001
defaultFunctions	0.005	0.000	0.006
defaultGenerator	0.074	0.002	0.075
extractQuality	0.000	0.000	0.001
feat2dens	1.054	0.128	1.183
featureDensity	0.002	0.000	0.002
makeFeatures	0.080	0.004	0.084
placeFeatures	0.105	0.000	0.106
pos2fastq	0.071	0.001	0.072
readError	0.003	0.000	0.003
reconcileFeatures	0.117	0.003	0.121
sampleReads	0.901	0.154	1.057
simChIP	0.001	0.000	0.001
simpleNames	0	0	0
stableFeature	0.000	0.000	0.001
writeFASTQ	0.001	0.000	0.001