Package: mBPCR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mBPCR_1.4.0.tar.gz

StartedAt: 2011-03-31 06:42:27 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:45:49 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 201.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: mBPCR.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/mBPCR.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mBPCR/DESCRIPTION’ ... OK
* this is package ‘mBPCR’ version ‘1.4.0’
* checking package name space information ...Warning: unknown namespace directive: importMethodFrom(SNPchip, centromere)
 OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘mBPCR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: unknown namespace directive: importMethodFrom(SNPchip, centromere)
  Warning: unknown namespace directive: importMethodFrom(SNPchip, centromere)
See ‘/Users/biocbuild/bbs-2.7-bioc/meat/mBPCR.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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 ... OK
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.7-bioc/meat/mBPCR.Rcheck/00check.log’
for details

* installing *source* package ‘mBPCR’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

================================================================================
Welcome to oligoClasses version 1.12.2
================================================================================
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 1.14.0
Warning: unknown namespace directive: importMethodFrom(SNPchip, centromere)
** help
*** installing help indices
** building package indices ...
Warning: unknown namespace directive: importMethodFrom(SNPchip, centromere)
** testing if installed package can be loaded

* DONE (mBPCR)

name	user	system	elapsed
computeMBPCR	8.626	0.099	10.185
estGlobParam	0.023	0.005	0.046
estProfileWithMBPCR	14.751	0.107	15.890
estProfileWithMBPCRforOligoSnpSet	0	0	0
importCNData	0.069	0.008	0.077
logAdd	0.001	0.000	0.000
plotEstProfile	30.022	0.155	30.541
writeEstProfile	14.030	0.078	14.264