BioC 2.9: CHECK report for SNPchip on moscato1

Package: SNPchip

Version: 1.17.0

Command: mkdir SNPchip.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SNPchip.buildbin-libdir SNPchip_1.17.0.tar.gz >SNPchip-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=SNPchip.buildbin-libdir --install="check:SNPchip-install.out" --force-multiarch --no-vignettes --timings SNPchip_1.17.0.tar.gz && mv SNPchip.buildbin-libdir/* SNPchip.Rcheck/ && rmdir SNPchip.buildbin-libdir

StartedAt: 2011-07-07 06:20:02 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:22:33 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 150.2 seconds

RetCode: 0

Status: OK

CheckDir: SNPchip.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/SNPchip.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SNPchip/DESCRIPTION' ... OK
* this is package 'SNPchip' version '1.17.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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
* loading checks for arch 'i386'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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
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
  ================================================================================
  Welcome to oligoClasses version 1.15.9
  ================================================================================
  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 tools::resaveRdaFiles() or R CMD build --resave-data
                      old_size new_size compress
  crlmmOut.RData         604Kb    425Kb       xz
  hapmap.RData           496Kb    430Kb       xz
  sample.snpset.RData    826Kb    496Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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


install for i386

* installing *source* package 'SNPchip' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
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
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
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 1.17.0

add DLL for x64

* installing *source* package 'SNPchip' ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
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 1.17.0
* MD5 sums
packaged installation of 'SNPchip' as SNPchip_1.17.0.zip

* DONE (SNPchip)

name	user	system	elapsed
ParESet-class	0	0	0
ParSnpCallSet-class	0	0	0
ParSnpCopyNumberSet-class	0	0	0
ParSnpSet-class	0	0	0
centromere	0.00	0.02	0.02
chromosomeAnnotation	0.01	0.00	0.01
chromosomeSize	0	0	0
crlmmOut	0.05	0.01	0.07
cytoband	0	0	0
dbSnpId	0	0	0
hapmap	0.03	0.00	0.03
integer2chromosome	0	0	0
plotCytoband	0.06	0.00	0.06
plotPredictions	0	0	0
plotSnp	0.47	0.00	0.47
sample.snpset	0.06	0.00	0.07
snpPar	0.28	0.00	0.28

Summary

Command output