BioC 2.13: CHECK report for chroGPS on perceval

Package: chroGPS

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chroGPS_1.6.1.tar.gz

StartedAt: 2014-04-05 00:21:06 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:23:29 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 143.3 seconds

RetCode: 0

Status:  OK

CheckDir: chroGPS.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/chroGPS.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chroGPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chroGPS’ version ‘1.6.1’
* 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 ‘chroGPS’ can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graphics’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘MASS’ ‘methods’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ calls which should be ‘::’:
  ‘changepoint:::cpt.var’ ‘changepoint:::plot’
  See the note in ?`:::` about the use of this operator.
Missing object imported by a ‘:::’ call: ‘changepoint:::cpt.method’
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
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import by ‘graphics::plot’ when loading ‘chroGPS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import by ‘graphics::plot’ when loading ‘chroGPS’
* DONE (chroGPS)

name	user	system	elapsed
addVar	0.004	0.001	0.005
adjustPeaks	0.006	0.001	0.006
boostMDS	0.007	0.002	0.008
clusGPS-class	0.236	0.001	0.237
clusGPS	0.013	0.001	0.016
distGPS-class	0.008	0.001	0.009
distGPS	0.060	0.003	0.063
domainDist	0.008	0.000	0.008
geneSetGPS	0.011	0.001	0.011
getURL	0.013	0.001	0.013
gff2RDList	0.008	0.000	0.009
gps2xgmml	0.004	0.000	0.004
mds-class	0.006	0.001	0.006
mds	0.033	0.001	0.035
mergeClusters	0.011	0.000	0.011
procrustesAdj	3.049	0.237	3.370
profileClusters	0.020	0.001	0.021
s2	0.941	0.018	0.961
splitDistGPS-class	0.006	0.005	0.010