BioC 3.1: CHECK report for geecc on morelia

Package: geecc

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geecc_1.2.0.tar.gz

StartedAt: 2015-10-09 02:08:30 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:09:37 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 66.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: geecc.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geecc_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/geecc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geecc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geecc’ 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 ‘geecc’ can be installed ... [1s/2s] 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
'library' or 'require' calls in package code:
  ‘AnnotationDbi’ ‘GO.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GO2level: no visible global function definition for ‘Term’
GO2level: no visible binding for global variable ‘GOTERM’
GO2list : <anonymous>: no visible global function definition for
  ‘Ontology’
GO2offspring: no visible binding for global variable ‘GOBPOFFSPRING’
GO2offspring: no visible binding for global variable ‘GOCCOFFSPRING’
GO2offspring: no visible binding for global variable ‘GOMFOFFSPRING’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘pval2star’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  marioni.rda    1.5Mb    1.0Mb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
GO2list 25.472  1.678  27.896
* 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 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/geecc.Rcheck/00check.log’
for details.

* installing *source* package ‘geecc’ ...
** 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 (geecc)

name	user	system	elapsed
GO2list	25.472	1.678	27.896
concub-class	0.002	0.000	0.002
concubfilter-class	0.002	0.001	0.002
filterConCub	0.001	0.000	0.000
geecc-package	0.343	0.010	0.355
marioni	0.059	0.001	0.061
plotConCub	0.339	0.012	0.355
runConCub	0.269	0.002	0.271