BioC 3.3: CHECK report for DEXSeq on linux2.bioconductor.org

Package: DEXSeq

Version: 1.17.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.17.0.tar.gz

StartedAt: 2015-10-27 03:21:28 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:25:09 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 221.6 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DEXSeq.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.17.0’
* 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 ... [11s/11s] 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’
Undefined global functions or variables:
  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 ... [97s/98s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
estimateExonFoldChanges 34.913  0.235  35.399
DEXSeq                  30.133  0.280  30.248
perGeneQValue            5.755  0.008   5.895
testForDEU               5.291  0.000   5.309
* 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-3.3-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
DEXSeq	30.133	0.280	30.248
DEXSeqDataSet	0.003	0.000	0.003
DEXSeqHTML	0	0	0
DEXSeqResults	4.689	0.048	4.737
accessors	0.087	0.004	0.091
counts	0.019	0.000	0.019
estimateDispersions	4.380	0.008	4.394
estimateExonFoldChanges	34.913	0.235	35.399
methods-gr	4.534	0.032	4.689
perGeneQValue	5.755	0.008	5.895
plotDEXSeq	0.001	0.000	0.001
plotMA	0.001	0.000	0.001
testForDEU	5.291	0.000	5.309