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BioC 3.2: CHECK report for DEXSeq on zin1

This page was generated on 2015-08-24 10:48:01 -0700 (Mon, 24 Aug 2015).

Package 266/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEXSeq 1.15.10
Alejandro Reyes
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEXSeq
Last Changed Rev: 106920 / Revision: 107696
Last Changed Date: 2015-07-30 09:03:53 -0700 (Thu, 30 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEXSeq
Version: 1.15.10
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.15.10.tar.gz
StartedAt: 2015-08-23 23:19:03 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 23:23:09 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 245.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DEXSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.15.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/DEXSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.15.10’
* 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 ... [14s/14s] 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 ... [102s/109s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DEXSeq                  30.995  0.739  32.870
estimateExonFoldChanges 30.836  0.831  36.292
methods-gr               6.226  0.491   6.701
DEXSeqResults            6.061  0.514   7.132
perGeneQValue            6.000  0.552   6.448
testForDEU               5.853  0.531   6.317
estimateDispersions      4.933  0.337   6.387
* 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
  ‘/home/biocbuild/bbs-3.2-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
DEXSeq30.995 0.73932.870
DEXSeqDataSet0.0020.0000.002
DEXSeqHTML0.0010.0000.001
DEXSeqResults6.0610.5147.132
accessors0.0800.0040.083
counts0.0140.0000.015
estimateDispersions4.9330.3376.387
estimateExonFoldChanges30.836 0.83136.292
methods-gr6.2260.4916.701
perGeneQValue6.0000.5526.448
plotDEXSeq0.0000.0000.001
plotMA0.0010.0000.001
testForDEU5.8530.5316.317