BioC 2.13: CHECK report for GGBase on zin1

Package: GGBase

Version: 3.24.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings GGBase_3.24.0.tar.gz

StartedAt: 2014-04-05 01:29:26 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:32:36 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 190.2 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GGBase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGBase/DESCRIPTION’ ... OK
* this is package ‘GGBase’ version ‘3.24.0’
* 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 ... [14s/14s] OK
* 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘snpStats’ which was already attached by Depends.
  Please remove these calls from your code.
Missing or unexported object: ‘snpStats::rbind2’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
MAFfilter 5.416  0.148   5.604
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘MAFfilter.R’ [12s/12s]
  Running ‘make.R’ [12s/12s]
  Running ‘plot_EvG.R’ [12s/12s]
 [37s/37s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	5.416	0.148	5.604
clipPCs	0.224	0.004	0.227
externalize	0.000	0.000	0.001
make_smlSet	3.833	0.088	3.930
plot_EvG	3.604	0.060	3.679
rsid-class	0.004	0.000	0.004
smlSet-class	0.000	0.000	0.003