BioC 3.3: CHECK report for lmdme on zin2

Package: lmdme

Version: 1.14.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings lmdme_1.14.0.tar.gz

StartedAt: 2016-10-13 03:44:57 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:45:47 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 50.0 seconds

RetCode: 0

Status:  OK

CheckDir: lmdme.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 lmdme_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/lmdme.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 ‘lmdme/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lmdme’ 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 ‘lmdme’ 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 ... NOTE
'library' or 'require' call to ‘parallel’ 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
biplot,lmdme : <anonymous>: no visible global function definition for
  ‘X11’
biplot,lmdme : <anonymous>: no visible global function definition for
  ‘par’
biplot,lmdme : <anonymous>: no visible global function definition for
  ‘abline’
decomposition,lmdme : <anonymous>: no visible global function
  definition for ‘prcomp’
decomposition,lmdme : <anonymous>: no visible global function
  definition for ‘model.matrix’
decomposition,lmdme : <anonymous>: no visible global function
  definition for ‘plsr’
fitted.values,lmdme : <anonymous>: no visible global function
  definition for ‘model.matrix’
fitted.values,lmdme : <anonymous>: no visible global function
  definition for ‘as.formula’
leverage,lmdme: no visible global function definition for ‘prcomp’
leverage,lmdme: no visible global function definition for ‘quantile’
lmdme,formula-ANY-data.frame : printnow: no visible global function
  definition for ‘flush.console’
lmdme,formula-ANY-data.frame: no visible global function definition for
  ‘terms’
lmdme,formula-ANY-data.frame: no visible binding for global variable
  ‘as.formula’
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for ‘model.matrix’
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for ‘as.formula’
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for ‘pt’
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for ‘pchisq’
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for ‘pf’
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for ‘terms’
loadingplot,lmdme: no visible global function definition for ‘loadings’
loadingplot,lmdme: no visible global function definition for ‘matplot’
loadingplot,lmdme: no visible global function definition for ‘box’
loadingplot,lmdme: no visible global function definition for ‘axis’
loadingplot,lmdme: no visible global function definition for ‘legend’
p.adjust,lmdme: no visible binding for global variable
  ‘p.adjust.methods’
permutation,formula-data.frame-data.frame : printnow: no visible global
  function definition for ‘flush.console’
permutation,formula-data.frame-data.frame: no visible binding for
  global variable ‘mclapply’
permutation,formula-data.frame-data.frame: no visible global function
  definition for ‘detectCores’
print,lmdme: no visible global function definition for ‘head’
print,lmdme: no visible global function definition for ‘pvalues’
print,lmdme: no visible binding for global variable ‘head’
screeplot,lmdme : <anonymous>: no visible global function definition
  for ‘X11’
screeplot,lmdme : <anonymous>: no visible global function definition
  for ‘par’
screeplot,lmdme: no visible global function definition for ‘plot’
screeplot,lmdme : <anonymous>: no visible global function definition
  for ‘lines’
screeplot,lmdme: no visible global function definition for ‘legend’
show,lmdme: no visible global function definition for ‘head’
Undefined global functions or variables:
  X11 abline as.formula axis box detectCores flush.console head legend
  lines loadings matplot mclapply model.matrix p.adjust.methods par
  pchisq pf plot plsr prcomp pt pvalues quantile terms
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "matplot", "par", "plot")
  importFrom("stats", "as.formula", "loadings", "model.matrix",
             "p.adjust.methods", "pchisq", "pf", "prcomp", "pt",
             "quantile", "terms")
  importFrom("utils", "flush.console", "head")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
lmdme-permutation 5.473  0.323   3.907
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/lmdme.Rcheck/00check.log’
for details.

* installing *source* package ‘lmdme’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘fitted.values’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘fitted’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘coef’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘coefficients’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘resid’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘residuals’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘print’ from package ‘base’ in package ‘lmdme’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘lmdme’
Creating a new generic function for ‘p.adjust’ in package ‘lmdme’
Creating a generic function for ‘biplot’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘screeplot’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘loadingplot’ from package ‘pls’ in package ‘lmdme’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lmdme)

name	user	system	elapsed
lmdme-biplot	3.130	0.051	3.215
lmdme-decomposition	2.683	0.004	2.688
lmdme-getters	2.695	0.008	2.705
lmdme-leverage	2.809	0.024	2.842
lmdme-lmdme	2.447	0.000	2.445
lmdme-loadingplot	2.571	0.020	2.593
lmdme-padjust	2.693	0.024	2.715
lmdme-permutation	5.473	0.323	3.907
lmdme-printshow	2.561	0.008	2.576
lmdme-screeplot	2.428	0.028	2.459