BioC 2.12: CHECK report for GGBase on petty

Package: GGBase

Version: 3.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGBase_3.22.0.tar.gz

StartedAt: 2013-10-08 22:34:18 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:41:14 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 415.9 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GGBase.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 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.22.0'
* 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 'GGBase' can be installed ... [31s/31s] 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 ... [40s/45s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
MAFfilter   10.221  0.548  14.749
make_smlSet  6.798  0.378   7.214
plot_EvG     6.426  0.452   6.925
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'MAFfilter.R' [25s/25s]
  Running 'make.R' [25s/25s]
  Running 'plot_EvG.R' [24s/24s]
 [74s/75s] 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
** testing if installed package can be loaded
* DONE (GGBase)

name	user	system	elapsed
MAFfilter	10.221	0.548	14.749
clipPCs	0.451	0.046	0.501
externalize	0.004	0.007	0.011
make_smlSet	6.798	0.378	7.214
plot_EvG	6.426	0.452	6.925
rsid-class	0.006	0.005	0.010
smlSet-class	0.004	0.006	0.010