Package: xmapcore

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xmapcore_1.12.0.tar.gz

StartedAt: 2013-03-25 01:37:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:39:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 104.4 seconds

RetCode: 0

Status:  OK

CheckDir: xmapcore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/xmapcore.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'xmapcore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'xmapcore' version '1.12.0'
* 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 whether package 'xmapcore' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 'xmapcore.all':
  'all.arrays' 'all.chromosomes' 'all.domains' 'all.est_exons'
  'all.est_genes' 'all.est_transcripts' 'all.exons' 'all.genes'
  'all.prediction_transcripts' 'all.probes' 'all.probesets'
  'all.proteins' 'all.symbols' 'all.synonyms' 'all.transcripts'

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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R'
 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/xmapcore.Rcheck/00check.log'
for details.

* installing *source* package 'xmapcore' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'INSTALL.Rnw' 
   'xmapcore.Rnw' 
** testing if installed package can be loaded

* DONE (xmapcore)

name	user	system	elapsed
xmapcore.all	0.000	0.000	0.001
xmapcore.coords	0.003	0.000	0.003
xmapcore.details	0	0	0
xmapcore.env	0	0	0
xmapcore.filters	0.000	0.000	0.001
xmapcore.range	0	0	0
xmapcore.to	0.000	0.000	0.001
xmapcore.utils	0	0	0
xmapcore.utr	0	0	0