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Package 121/658HostnameOS / ArchBUILDCHECKBUILD BIN
chroGPS 1.1.0
Oscar Reina
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chroGPS
Last Changed Rev: 70052 / Revision: 74756
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: chroGPS
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chroGPS_1.1.0.tar.gz
StartedAt: 2013-03-24 03:42:02 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 03:44:50 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 168.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: chroGPS.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/chroGPS.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* 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 '1.1.0'
* 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/14s] 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 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 installed files from 'inst/doc' ... OK
* checking examples ... [17s/18s] WARNING
Found the following significant warnings:

  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
  Warning: %in% between a RangedData and a RangedData object is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
sl2 7.765  0.114   8.647
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/chroGPS.Rcheck/00check.log'
for details.

chroGPS.Rcheck/00install.out:

* 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
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
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (chroGPS)

chroGPS.Rcheck/chroGPS-Ex.timings:

nameusersystemelapsed
addVar0.0090.0020.011
adjustPeaks0.0060.0010.007
boostMDS0.0120.0020.017
clusGPS-class0.0070.0020.009
clusGPS0.0100.0040.018
distGPS-class0.0060.0020.009
distGPS0.0790.0090.093
domainDist0.0150.0020.023
geneSample0.0420.0060.049
geneSetGPS0.0240.0020.031
getURL0.0110.0000.012
gff2RDList0.0120.0020.017
mds-class0.0110.0020.014
mds0.0350.0050.041
procrustesAdj2.2050.0272.383
sl27.7650.1148.647
splitDistGPS-class0.0030.0050.009