Package: chroGPS

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chroGPS_1.3.0.tar.gz

StartedAt: 2013-05-01 03:48:14 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 03:51:10 -0700 (Wed, 01 May 2013)

EllapsedTime: 176.2 seconds

RetCode: 0

Status:  OK

CheckDir: chroGPS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/chroGPS.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'chroGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chroGPS' version '1.3.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'chroGPS' can be installed ... [13s/15s] 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
contour2dDP: no visible binding for global variable 'state'
gps2xgmml: no visible global function definition for 'col2hex'
uniqueCount: no visible binding for global variable 'u'
xgmml2d: no visible global function definition for 'xmlOutputDOM'
xgmml2d: no visible global function definition for 'saveXML'
xgmml3d: no visible global function definition for 'xmlOutputDOM'
xgmml3d: no visible global function definition for 'saveXML'
gps2xgmml,mds: no visible global function definition for 'col2hex'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [12s/23s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
procrustesAdj 3.178  0.429   14.27
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'gplots'
* 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-2.12-bioc/meat/chroGPS.Rcheck/00check.log'
for details.

* installing *source* package 'chroGPS' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
* DONE (chroGPS)

name	user	system	elapsed
addVar	0.007	0.000	0.008
adjustPeaks	0.008	0.001	0.008
boostMDS	0.013	0.002	0.015
clusGPS-class	0.010	0.001	0.011
clusGPS	0.018	0.001	0.019
distGPS-class	0.009	0.001	0.009
distGPS	0.262	0.004	0.266
domainDist	0.008	0.002	0.010
geneSetGPS	0.011	0.003	0.015
getURL	0.009	0.003	0.011
gff2RDList	0.008	0.002	0.010
gps2xgmml	0.009	0.002	0.011
mds-class	0.188	0.002	0.190
mds	0.029	0.004	0.034
mergeClusters	0.014	0.004	0.019
procrustesAdj	3.178	0.429	14.270
profileClusters	0.036	0.002	0.038
s2	1.119	0.028	1.227
splitDistGPS-class	0.007	0.005	0.012