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BioC 3.1: CHECK report for DEXSeq on petty

This page was generated on 2015-10-09 09:34:34 -0700 (Fri, 09 Oct 2015).

Package 257/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEXSeq 1.14.2
Alejandro Reyes
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/DEXSeq
Last Changed Rev: 107759 / Revision: 109384
Last Changed Date: 2015-08-25 07:01:10 -0700 (Tue, 25 Aug 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEXSeq
Version: 1.14.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.14.2.tar.gz
StartedAt: 2015-10-08 22:34:26 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:40:55 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 388.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DEXSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/DEXSeq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.14.2’
* 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 ... [24s/24s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [151s/150s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
estimateExonFoldChanges 48.766  1.024  49.280
DEXSeq                  47.517  1.186  48.220
methods-gr               9.139  0.189   9.339
perGeneQValue            9.022  0.028   9.064
DEXSeqResults            7.817  0.023   7.849
testForDEU               6.998  0.009   7.022
estimateDispersions      6.319  0.080   6.400
* 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.


DEXSeq.Rcheck/00install.out:

* installing *source* package ‘DEXSeq’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DEXSeq)

DEXSeq.Rcheck/DEXSeq-Ex.timings:

nameusersystemelapsed
DEXSeq47.517 1.18648.220
DEXSeqDataSet0.0050.0010.006
DEXSeqHTML0.0010.0000.001
DEXSeqResults7.8170.0237.849
accessors0.0910.0020.092
counts0.0160.0010.017
estimateDispersions6.3190.0806.400
estimateExonFoldChanges48.766 1.02449.280
methods-gr9.1390.1899.339
perGeneQValue9.0220.0289.064
plotDEXSeq0.0020.0000.003
plotMA0.0020.0000.002
testForDEU6.9980.0097.022