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BioC 3.0: CHECK report for SCAN.UPC on oaxaca

This page was generated on 2015-04-10 10:06:25 -0700 (Fri, 10 Apr 2015).

Package 803/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCAN.UPC 2.8.1
Stephen R. Piccolo
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SCAN.UPC
Last Changed Rev: 99152 / Revision: 102249
Last Changed Date: 2015-02-06 12:47:44 -0800 (Fri, 06 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: SCAN.UPC
Version: 2.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SCAN.UPC_2.8.1.tar.gz
StartedAt: 2015-04-10 03:14:11 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:19:22 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 310.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SCAN.UPC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SCAN.UPC_2.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SCAN.UPC.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.8.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘oligo’ ‘Biostrings’ ‘GEOquery’ ‘affy’ ‘affyio’ ‘foreach’
  ‘sva’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [30s/32s] 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 loading without being on the library search path ... OK
* checking 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
BatchAdjust: no visible global function definition for ‘varLabels’
BatchAdjust: no visible global function definition for ‘exprs<-’
BatchAdjust: no visible global function definition for ‘pData’
BatchAdjustFromFile: no visible global function definition for
  ‘sampleNames’
BatchAdjustFromFile: no visible global function definition for ‘pData’
BatchAdjustFromFile: no visible global function definition for
  ‘varLabels’
BatchAdjustFromFile: no visible global function definition for
  ‘pData<-’
ProcessGtfSubset: no visible global function definition for ‘IRanges’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘pData’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘featureData’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘DNAStringSet’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘exprs<-’
UPC_RNASeq: no visible global function definition for ‘sampleNames<-’
UPC_RNASeq: no visible global function definition for ‘featureNames<-’
processCelFiles: no visible global function definition for ‘%dopar%’
processCelFiles: no visible global function definition for
  ‘sampleNames<-’
processCelFiles: no visible global function definition for
  ‘featureNames<-’
processTwoColor: no visible global function definition for
  ‘sampleNames<-’
processTwoColor: no visible global function definition for
  ‘featureNames<-’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] 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
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/SCAN.UPC.Rcheck/00check.log’
for details.

SCAN.UPC.Rcheck/00install.out:

* 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)
================================================================================
** 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)
================================================================================
* DONE (SCAN.UPC)

SCAN.UPC.Rcheck/SCAN.UPC-Ex.timings:

nameusersystemelapsed
InstallBrainArrayPackage0.0010.0000.000
ParseMetaFromGtfFile0.0000.0000.001
SCAN0.0010.0000.002
SCAN_TwoColor0.0000.0000.001
UPC_Generic_ExpressionSet0.0010.0000.000
UPC_RNASeq0.0010.0010.001
UPC_TwoColor0.0000.0000.001