BioC 3.2: CHECK report for les on perceval

Package: les

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings les_1.20.0.tar.gz

StartedAt: 2015-10-27 09:18:53 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:20:03 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 70.0 seconds

RetCode: 0

Status:  OK

CheckDir: les.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 les_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/les.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘les/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘les’ version ‘1.20.0’
* 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 ‘les’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Package in Depends field not imported from: ‘fdrtool’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘stats:::lm.wfit’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘calcSingle’ ‘cdfDuplicates’ ‘checkState’ ‘diagSquare’ ‘fitGsri’
  ‘gsri’ ‘itLinReg’ ‘mcsapply’ ‘modGrenander’ ‘qrSlope’ ‘reg2log’
  ‘seSlopeWeight’ ‘setState’ ‘slopeWeight’ ‘wcdf2’ ‘wcdfGrenander’
  ‘xvalWeight’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("C_isomean", ..., PACKAGE = "fdrtool")
Call with DUP:
   .C("C_isomean", as.double(rawslope), as.double(dx), as.integer(n), 
       ghat = double(n), PACKAGE = "fdrtool", DUP = FALSE)
DUP is no longer supported and will be ignored.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
les-package 20.297  0.228  20.530
ci          14.632  0.141  14.773
chi2         6.648  0.122   6.770
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/les.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Les-class	0.003	0.000	0.003
Les	0.064	0.003	0.066
chi2	6.648	0.122	6.770
ci	14.632	0.141	14.773
estimate	0.495	0.004	0.498
export	0.001	0.000	0.001
les-package	20.297	0.228	20.530
plot	0.506	0.003	0.509
regions	0.515	0.001	0.516
threshold	0.538	0.002	0.540
weighting	0.008	0.002	0.010