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BioC 2.12: CHECK report for chroGPS on george2

This page was generated on 2013-10-09 09:37:57 -0700 (Wed, 09 Oct 2013).

Package 122/671HostnameOS / ArchBUILDCHECKBUILD BIN
chroGPS 1.3.3
Oscar Reina
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/chroGPS
Last Changed Rev: 80400 / Revision: 81334
Last Changed Date: 2013-09-13 06:32:28 -0700 (Fri, 13 Sep 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: chroGPS
Version: 1.3.3
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings chroGPS_1.3.3.tar.gz
StartedAt: 2013-10-09 00:53:35 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:57:02 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 207.3 seconds
RetCode: 0
Status:  OK 
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/chroGPS.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.3.3’
* 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 ... [16s/19s] 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 ... [14s/16s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/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: replacing previous import ‘plot’ when loading ‘graphics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘plot’ when loading ‘graphics’
* DONE (chroGPS)

chroGPS.Rcheck/chroGPS-Ex.timings:

nameusersystemelapsed
addVar0.0040.0040.011
adjustPeaks0.0160.0000.015
boostMDS0.0200.0000.023
clusGPS-class0.0160.0000.019
clusGPS0.0240.0040.026
distGPS-class0.0200.0000.035
distGPS0.4640.0040.574
domainDist0.0120.0000.015
geneSetGPS0.020.000.02
getURL0.0080.0000.008
gff2RDList0.0120.0080.020
gps2xgmml0.0120.0000.012
mds-class0.0240.0000.022
mds0.0720.0000.071
mergeClusters0.3520.0000.378
procrustesAdj3.2720.1163.832
profileClusters0.0600.0000.061
s21.4600.0081.482
splitDistGPS-class0.0120.0000.014