BioC 2.12: CHECK report for a4Reporting on petty

Package: a4Reporting

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Reporting_1.8.0.tar.gz

StartedAt: 2013-10-08 21:26:57 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:29:44 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 166.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: a4Reporting.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/a4Reporting.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'a4Reporting/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Reporting' 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 'a4Reporting' can be installed ... [16s/17s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-bioc/meat/a4Reporting.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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 for unstated 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 ... 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 ... NOTE
S3 methods shown with full name in documentation object 'print.xtableAnnotationTable':
  'print.xtableAnnotationTable'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.annotationTable.R' [10s/10s]
 [11s/11s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/a4Reporting.Rcheck/00check.log'
for details.

* installing *source* package 'a4Reporting' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
* DONE (a4Reporting)

name	user	system	elapsed
annotationTable-class	0.013	0.001	0.012
annotationTable	0.017	0.000	0.018
xtable-methods	0.050	0.001	0.051