Package: chroGPS

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chroGPS_1.0.1.tar.gz

StartedAt: 2013-03-24 22:59:51 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:02:13 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 142.6 seconds

RetCode: 0

Status:  OK

CheckDir: chroGPS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/chroGPS.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 'chroGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chroGPS' version '1.0.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'chroGPS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
* 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 ... NOTE
contour2dDP: no visible binding for global variable 'state'
contour3dDP: no visible global function definition for 'ssden'
contour3dDP: no visible global function definition for 'dssden'
contour3dDP: no visible global function definition for 'convhulln'
contour3dDP: no visible binding for global variable 'type'
domainDist: no visible global function definition for 'combs'
enrichmentClusGPS: no visible global function definition for 'barplot2'
uniqueCount: no visible binding for global variable 'u'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
sl2 4.972  0.117   5.451
* 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 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/chroGPS.Rcheck/00check.log'
for details.

* installing *source* package 'chroGPS' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'chroGPS'
** help
*** installing help indices
** building package indices
** installing vignettes
   'chroGPS.Rnw' 
** testing if installed package can be loaded

* DONE (chroGPS)

name	user	system	elapsed
addVar	0	0	0
adjustPeaks	0.000	0.000	0.001
boostMDS	0	0	0
clusGPS-class	0.001	0.000	0.001
clusGPS	0	0	0
distGPS-class	0.000	0.001	0.002
distGPS	0.052	0.005	0.075
domainDist	0	0	0
geneSample	0.028	0.007	0.040
geneSetGPS	0	0	0
getURL	0	0	0
gff2RDList	0	0	0
mds-class	0.001	0.000	0.000
mds	0.012	0.002	0.014
procrustesAdj	1.804	0.022	1.876
sl2	4.972	0.117	5.451
splitDistGPS-class	0	0	0