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BioC 3.0: CHECK report for DEXSeq on zin1

This page was generated on 2015-04-10 09:39:26 -0700 (Fri, 10 Apr 2015).

Package 239/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEXSeq 1.12.2
Alejandro Reyes
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/DEXSeq
Last Changed Rev: 99750 / Revision: 102249
Last Changed Date: 2015-02-24 06:45:35 -0800 (Tue, 24 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DEXSeq
Version: 1.12.2
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.12.2.tar.gz
StartedAt: 2015-04-09 23:19:03 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:22:59 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 236.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DEXSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/DEXSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.12.2’
* 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 ‘DEXSeq’ can be installed ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEXSeqDataSet: no visible global function definition for ‘DataFrame’
estimateExonFoldChanges: no visible global function definition for
  ‘DataFrame’
show.DEXSeqResults: no visible global function definition for
  ‘DataFrame’
show,DEXSeqResults: no visible global function definition for
  ‘DataFrame’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DEXSeq                  7.653  0.024   7.724
estimateExonFoldChanges 6.885  0.012   6.907
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

DEXSeq.Rcheck/00install.out:

* installing *source* package ‘DEXSeq’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEXSeq)

DEXSeq.Rcheck/DEXSeq-Ex.timings:

nameusersystemelapsed
DEXSeq7.6530.0247.724
DEXSeqDataSet0.0000.0000.003
DEXSeqHTML0.0000.0000.001
DEXSeqResults4.6320.0044.642
accessors0.0720.0040.076
counts0.0120.0000.011
estimateDispersions4.0000.0044.014
estimateExonFoldChanges6.8850.0126.907
methods-gr4.8360.0084.852
perGeneQValue4.7400.0044.756
plotDEXSeq0.0000.0000.001
plotMA0.0000.0000.001
testForDEU4.9480.0004.993