BioC 3.2: CHECK report for SwimR on zin1

Package: SwimR

Version: 1.8.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SwimR_1.8.0.tar.gz

StartedAt: 2016-04-23 05:56:22 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:57:00 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 37.9 seconds

RetCode: 0

Status:  OK

CheckDir: SwimR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SwimR_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SwimR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SwimR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SwimR’ version ‘1.8.0’
* 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 ‘SwimR’ can be installed ... [1s/1s] OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘R2HTML’ ‘gplots’ ‘heatmap.plus’ ‘signal’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘R2HTML’ ‘gplots’ ‘heatmap.plus’ ‘methods’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SwimR: no visible global function definition for ‘colorpanel’
SwimR: no visible global function definition for ‘heatmap.plus’
SwimR: no visible global function definition for ‘HTMLInitFile’
SwimR: no visible global function definition for ‘HTML’
SwimR: no visible global function definition for ‘HTMLEndFile’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
  definition for ‘fir1’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
  definition for ‘as.Arma’
createFrequencyMatrix : FrequencyAnalysis: no visible global function
  definition for ‘hamming’
createFrequencyMatrix: no visible global function definition for
  ‘HTMLInitFile’
createFrequencyMatrix: no visible global function definition for ‘HTML’
createFrequencyMatrix: no visible global function definition for
  ‘HTMLEndFile’
* 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 ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
createFrequencyMatrix 14.088  0.020  14.154
SwimR                  8.502  0.051   8.569
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/SwimR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
SwimR	8.502	0.051	8.569
createFrequencyMatrix	14.088	0.020	14.154