BioC 3.2: CHECK report for rGREAT on perceval

Package: rGREAT

Version: 1.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rGREAT_1.1.4.tar.gz

StartedAt: 2015-08-24 04:32:48 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:35:12 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 144.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: rGREAT.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rGREAT_1.1.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rGREAT.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 ‘rGREAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rGREAT’ version ‘1.1.4’
* 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 ‘rGREAT’ can be installed ... [11s/11s] WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.2-bioc/meat/rGREAT.Rcheck/00_pkg_src/rGREAT/man/getEnrichmentTables-GreatJob-method.rd:14: All text must be in a section
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/rGREAT.Rcheck/00install.out’ for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
prepare_Rd: getEnrichmentTables-GreatJob-method.rd:14: All text must be in a section
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GreatJob’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/19s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
submitGreatJob 0.365  0.022  12.862
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [6s/6s]
 [6s/6s] 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: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/rGREAT.Rcheck/00check.log’
for details.

* installing *source* package ‘rGREAT’ ...
** R
** inst
** preparing package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.2-bioc/meat/rGREAT.Rcheck/00_pkg_src/rGREAT/man/getEnrichmentTables-GreatJob-method.rd:14: All text must be in a section
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rGREAT)

name	user	system	elapsed
GreatJob-class	0.001	0.000	0.000
availableCategories-GreatJob-method	0.043	0.004	0.048
availableOntologies-GreatJob-method	0.040	0.003	0.043
getEnrichmentTables-GreatJob-method	0.131	0.005	0.136
plotRegionGeneAssociationGraphs-GreatJob-method	0.576	0.028	0.617
submitGreatJob	0.365	0.022	12.862