Package: GGBase

Version: 3.21.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGBase_3.21.2.tar.gz

StartedAt: 2013-03-25 02:44:11 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:49:19 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 308.2 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GGBase.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.21.2'
* 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 'GGBase' can be installed ... [23s/23s] OK
* 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 ... NOTE
.oldcode : <anonymous>: warning in axis(3, at = genePosition(x@gene,
  annlib = x@annotation), col = "red", lwd = 2, label = " "): partial
  argument match of 'label' to 'labels'
.oldcode : pedinf2df: warning in read.table(fn, h = FALSE): partial
  argument match of 'h' to 'header'
allsnps: warning in dir(system.file("parts", package = packname), full
  = TRUE): partial argument match of 'full' to 'full.names'
.oldcode : genePosition: no visible global function definition for
  'revmap'
.oldcode : featureFilter: no visible global function definition for
  'keys'
.oldcode : sym2pid: no visible global function definition for 'revmap'
.oldcode : <anonymous>: no visible global function definition for
  'revmap'
.oldcode : snpLocs.Hsapiens: no visible global function definition for
  'getSNPlocs'
sym2pid: no visible global function definition for 'revmap'
plot_EvG,genesym-rsid-smlSet: no visible global function definition for
  'revmap'
* 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 examples ... [31s/32s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MAFfilter   8.086  0.507   8.722
make_smlSet 5.405  0.310   5.720
plot_EvG    5.289  0.344   5.666
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'MAFfilter.R' [18s/18s]
  Running 'make.R' [17s/17s]
  Running 'plot_EvG.R' [18s/18s]
 [53s/53s] 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GGBase.Rcheck/00check.log'
for details.

* installing *source* package 'GGBase' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ggbase.Rnw' 
** testing if installed package can be loaded
* DONE (GGBase)

name	user	system	elapsed
MAFfilter	8.086	0.507	8.722
clipPCs	0.016	0.009	0.026
externalize	0.003	0.006	0.009
make_smlSet	5.405	0.310	5.720
plot_EvG	5.289	0.344	5.666
rsid-class	0.004	0.004	0.009
smlSet-class	0.004	0.005	0.009