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