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Package 467/516HostnameOS / ArchBUILDCHECKBUILD BIN
SNPchip 1.18.1
Robert Scharpf
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/SNPchip
Last Changed Rev: 60425 / Revision: 61898
Last Changed Date: 2011-11-16 18:16:38 -0800 (Wed, 16 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 

Summary

Package: SNPchip
Version: 1.18.1
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch SNPchip_1.18.1.tar.gz
StartedAt: 2012-01-09 05:46:53 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 05:48:54 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 120.4 seconds
RetCode: 0
Status:  OK  
CheckDir: SNPchip.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/SNPchip.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SNPchip/DESCRIPTION' ... OK
* this is package 'SNPchip' version '1.18.1'
* 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 whether package 'SNPchip' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
File 'SNPchip/R/zzz.R':
  .onLoad calls:
    require("methods")
  .onAttach calls:
    message("Welcome to SNPchip version ", packageDescription(THISPKG,     field = "Version"))

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in ?.onAttach.

plotCytoband: no visible binding for global variable 'lsegments'
plotCytoband: no visible binding for global variable 'lpolygon'
* checking Rd files ... NOTE
prepare_Rd: sample.snpset.Rd:10-11: Dropping empty section \details
prepare_Rd: sample.snpset.Rd:12-13: Dropping empty section \source
prepare_Rd: sample.snpset.Rd:14-15: Dropping empty section \references
prepare_Rd: showSummary.Rd:21-22: Dropping empty section \details
prepare_Rd: showSummary.Rd:23-24: Dropping empty section \value
prepare_Rd: showSummary.Rd:27-28: Dropping empty section \note
prepare_Rd: showSummary.Rd:25: Dropping empty section \references
prepare_Rd: showSummary.Rd:31-32: 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  ================================================================================
  Large dataset support for 'oligo/crlmm': Disabled
       - Load 'ff'
  ================================================================================
  Parallel computing support for 'oligo/crlmm': Disabled
       - Load 'ff'
       - Load 'snow'
       - Use options(cluster=makeCluster(...))
  ================================================================================
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                      old_size new_size compress
  crlmmOut.RData         604Kb    426Kb       xz
  hapmap.RData           496Kb    430Kb       xz
  sample.snpset.RData    826Kb    493Kb       xz
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

SNPchip.Rcheck/00install.out:

* installing *source* package 'SNPchip' ...
** R
** data
** inst
** preparing package for lazy loading
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Creating a generic function for 'summary' from package 'base' in package 'SNPchip'
Creating a generic function for 'plot' from package 'graphics' in package 'SNPchip'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'SNPchip.Rnw' 
** testing if installed package can be loaded
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Welcome to SNPchip version 1.18.1

* DONE (SNPchip)

SNPchip.Rcheck/SNPchip-Ex.timings:

nameusersystemelapsed
ParESet-class000
ParSnpCallSet-class000
ParSnpCopyNumberSet-class000
ParSnpSet-class000
centromere000
chromosomeAnnotation0.030.000.03
chromosomeSize000
crlmmOut0.050.000.04
cytoband0.020.000.02
dbSnpId000
hapmap0.030.000.03
integer2chromosome000
plotCytoband0.060.000.06
plotPredictions000
plotSnp0.450.000.46
sample.snpset0.280.000.28
snpPar0.140.000.14