BioC 3.4: CHECK report for DEFormats on zin1

Package: DEFormats

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEFormats_1.1.2.tar.gz

StartedAt: 2016-09-20 05:26:13 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:28:13 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 119.8 seconds

RetCode: 0

Status:  OK

CheckDir: DEFormats.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEFormats_1.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DEFormats.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEFormats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEFormats’ version ‘1.1.2’
* package encoding: UTF-8
* 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 ‘DEFormats’ can be installed ... 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
as.DESeqDataSet.DGEList: no visible global function definition for ‘as’
as.DGEList.DESeqDataSet: no visible global function definition for ‘as’
simulateRnaSeqData: no visible global function definition for ‘as’
DGEList,RangedSummarizedExperiment: no visible global function
  definition for ‘new’
Undefined global functions or variables:
  as new
Consider adding
  importFrom("methods", "as", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/DEFormats.Rcheck/00check.log’
for details.

* installing *source* package ‘DEFormats’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘DGEList’ from ‘edgeR’ in package ‘DEFormats’
    (from the saved implicit definition)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEFormats)

name	user	system	elapsed
DGEList	0.156	0.000	0.156
as.DESeqDataSet	0.184	0.000	0.183
as.DGEList	0.448	0.000	0.449
simulateNormFactors	0.204	0.008	0.216
simulateRnaSeqData	0.116	0.004	0.117