Package: unifiedWMWqPCR

Version: 1.14.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings unifiedWMWqPCR_1.14.0.tar.gz

StartedAt: 2018-04-12 03:30:19 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:31:12 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 53.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: unifiedWMWqPCR.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings unifiedWMWqPCR_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/unifiedWMWqPCR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘unifiedWMWqPCR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘unifiedWMWqPCR’ version ‘1.14.0’
* 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 ‘unifiedWMWqPCR’ 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 loading without being on the library search path ... 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
.uWMW: no visible global function definition for ‘pnorm’
.volcano: no visible global function definition for ‘text’
forestplot.internal: no visible global function definition for ‘par’
forestplot.internal: no visible global function definition for ‘abline’
forestplot.internal: no visible global function definition for
  ‘strheight’
forestplot.internal: no visible global function definition for
  ‘segments’
forestplot.internal: no visible global function definition for
  ‘polygon’
forestplot.internal: no visible global function definition for ‘text’
forestplot.internal: no visible global function definition for ‘axis’
forestplot.internal: no visible global function definition for ‘mtext’
forestplot.internal: no visible global function definition for ‘points’
sandwich1.f: no visible global function definition for ‘na.omit’
sandwich2.f: no visible global function definition for ‘na.omit’
sandwich3.f: no visible global function definition for ‘na.omit’
getEstimate,uwmwRes: no visible global function definition for ‘qnorm’
getEstimate,uwmwRes: no visible global function definition for ‘plogis’
uWMW,qPCRset: no visible global function definition for ‘exprs’
Undefined global functions or variables:
  abline axis exprs mtext na.omit par plogis pnorm points polygon qnorm
  segments strheight text
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "points",
             "polygon", "segments", "strheight", "text")
  importFrom("stats", "na.omit", "plogis", "pnorm", "qnorm")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'uwmwRes,character'
  generic 'getEstimate' and siglist 'uwmwRes'
  generic 'sort' and siglist 'uwmwRes'
  generic 'type' and siglist 'uwmwRes'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'type':
is.unsorted
  Code: function(x, na.rm = FALSE, strictly = FALSE)
  Docs: function(x, na.rm = FALSE, strictly = FALSE, ...)
  Argument names in docs not in code:
    ...

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'getEstimate':
  ‘\S4method{getEstimate}{uwmwRes}’

Undocumented arguments in documentation object 'unorder'
  ‘method’
Objects in \usage without \alias in documentation object 'unorder':
  ‘\S4method{sort}{uwmwRes}’

Undocumented arguments in documentation object 'type'
  ‘...’
Objects in \usage without \alias in documentation object 'type':
  ‘\S4method{type}{uwmwRes}’

Objects in \usage without \alias in documentation object 'uwmw_Extract':
  ‘\S4method{[}{uwmwRes,character}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/unifiedWMWqPCR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
NBdata	0.056	0.000	0.056
as.matrix.uwmwEstimate	0.444	0.012	0.456
as.matrix.uwmwRes	0.472	0.004	0.476
forestplot-methods	0.688	0.012	0.701
getEstimate-methods	0.436	0.008	0.443
plot	0.384	0.000	0.384
sort.uwmwRes	0.372	0.004	0.374
uWMW-methods	0.836	0.000	0.836
uwmw_Accessors	0.352	0.000	0.350
uwmw_Extract	0.272	0.000	0.274
volcanopar	0	0	0
volcanoplot-methods	0.356	0.008	0.367