BioC 3.1: CHECK report for plethy on petty

Package: plethy

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings plethy_1.6.0.tar.gz

StartedAt: 2015-10-09 01:07:48 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:13:31 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 342.7 seconds

RetCode: 0

Status:  OK

CheckDir: plethy.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 plethy_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/plethy.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plethy/DESCRIPTION’ ... OK
* this is package ‘plethy’ version ‘1.6.0’
* 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 ‘plethy’ can be installed ... [12s/12s] 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
tsplot,BuxcoDB : .local: no visible binding for global variable ‘Days’
tsplot,BuxcoDB : .local: no visible binding for global variable ‘Value’
tsplot,BuxcoDB : .local: no visible binding for global variable
  ‘Sample_Name’
* 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 ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
utilities 13.239  1.896  15.541
parsing    6.288  1.464   7.965
plethy     6.131  1.438   7.640
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [174s/177s]
 [175s/177s] 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-3.1-bioc/meat/plethy.Rcheck/00check.log’
for details.

* installing *source* package ‘plethy’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (plethy)

name	user	system	elapsed
BuxcoDB	1.542	0.092	1.653
add_query_funcs	0.603	0.041	0.649
dbImport	0.673	0.032	0.745
parsing	6.288	1.464	7.965
plethy	6.131	1.438	7.640
utilities	13.239	1.896	15.541