BioC 2.13: CHECK report for SCAN.UPC on perceval

Package: SCAN.UPC

Version: 2.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SCAN.UPC_2.4.2.tar.gz

StartedAt: 2014-04-05 04:15:29 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:19:51 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 262.7 seconds

RetCode: 0

Status:  OK

CheckDir: SCAN.UPC.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/SCAN.UPC.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SCAN.UPC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SCAN.UPC’ version ‘2.4.2’
* 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 ‘SCAN.UPC’ can be installed ... [25s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need ‘+ file LICENSE’:
  MIT
* 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
Packages in Depends field not imported from:
  ‘affy’ ‘affyio’ ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... OK
* checking Rd files ... NOTE
prepare_Rd: SCAN.Rd:49-50: Dropping empty section \details
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘SCAN.vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/SCAN.UPC.Rcheck/00check.log’
for details.

* installing *source* package ‘SCAN.UPC’ ...
** R
** inst
** preparing package for lazy loading
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
Warning: replacing previous import by ‘oligo::show’ when loading ‘SCAN.UPC’
Warning: replacing previous import by ‘GEOquery::getGEOSuppFiles’ when loading ‘SCAN.UPC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
Warning: replacing previous import by ‘oligo::show’ when loading ‘SCAN.UPC’
Warning: replacing previous import by ‘GEOquery::getGEOSuppFiles’ when loading ‘SCAN.UPC’
* DONE (SCAN.UPC)

name	user	system	elapsed
InstallBrainArrayPackage	0.430	0.003	0.436
ParseMetaFromGtfFile	0.006	0.001	0.008
SCAN	0.015	0.005	0.021
SCAN_TwoColor	0.013	0.003	0.016
UPC_RNASeq	0.008	0.002	0.010
UPC_TwoColor	0.010	0.000	0.011