BioC 3.2: CHECK report for PROPER on oaxaca

Package: PROPER

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PROPER_1.2.0.tar.gz

StartedAt: 2016-04-23 03:15:39 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:16:29 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 49.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PROPER.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PROPER_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PROPER.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PROPER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PROPER’ version ‘1.2.0’
* 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 ‘PROPER’ can be installed ... [2s/3s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘edgeR’
'library' or 'require' call to ‘edgeR’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estParam: no visible global function definition for ‘exprs’
run.DESeq: no visible global function definition for ‘newCountDataSet’
run.DESeq: no visible global function definition for
  ‘estimateSizeFactors’
run.DESeq: no visible global function definition for
  ‘estimateDispersions’
run.DESeq: no visible global function definition for ‘nbinomTest’
run.DSS: no visible global function definition for ‘newSeqCountSet’
run.DSS: no visible global function definition for ‘estNormFactors’
run.DSS: no visible global function definition for ‘estDispersion’
run.DSS: no visible global function definition for ‘waldTest’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estParam':
estParam
  Code: function(X, type = 1)
  Docs: function(X, type = c(1, 2))
  Mismatches in argument default values:
    Name: 'type' Code: 1 Docs: c(1, 2)

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
runSims 15.898  0.813  16.739
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PROPER.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RNAseq.SimOptions.2grp	0.602	0.024	0.627
comparePower	0.002	0.001	0.003
estParam	0.001	0.000	0.000
plotPowerHist	0.000	0.000	0.001
plots	0.001	0.000	0.001
power.seqDepth	0	0	0
runSims	15.898	0.813	16.739
simRNAseq	0.354	0.024	0.379
summaryPower	0.000	0.000	0.001