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BioC 2.14: CHECK report for SNPchip on zin2

This page was generated on 2014-10-08 08:47:58 -0700 (Wed, 08 Oct 2014).

Package 737/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPchip 2.10.0
Robert Scharpf
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/SNPchip
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: SNPchip
Version: 2.10.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SNPchip_2.10.0.tar.gz
StartedAt: 2014-10-08 02:53:29 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:55:58 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 149.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SNPchip.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SNPchip_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/SNPchip.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPchip/DESCRIPTION’ ... OK
* this is package ‘SNPchip’ version ‘2.10.0’
* 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 ‘SNPchip’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
':::' call which should be '::': ‘lattice:::xyplot’
  See the note in ?`:::` about the use of this operator.
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
dataFrameSummarizedExperiment: no visible binding for global variable
  ‘j’
* checking Rd files ... NOTE
prepare_Rd: arrangeFigs.Rd:35-36: Dropping empty section \examples
prepare_Rd: dataFrame.Rd:43-44: Dropping empty section \examples
prepare_Rd: latticeFigs.Rd:27-29: Dropping empty section \details
prepare_Rd: latticeFigs.Rd:37-38: Dropping empty section \seealso
prepare_Rd: latticeFigs.Rd:39-40: Dropping empty section \examples
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
xyplotLrrBaf 8.661  0.096   8.788
xyplot       7.128  0.092   7.380
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [13s/13s]
 [13s/13s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/SNPchip.Rcheck/00check.log’
for details.

SNPchip.Rcheck/00install.out:

* installing *source* package ‘SNPchip’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPchip)

SNPchip.Rcheck/SNPchip-Ex.timings:

nameusersystemelapsed
centromere0.4760.0040.481
getCytoband0.0360.0000.033
plotIdiogram0.5680.0440.613
xypanel0.0000.0000.001
xyplot7.1280.0927.380
xyplotLrrBaf8.6610.0968.788