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CHECK report for lmdme on malbec1

This page was generated on 2019-04-16 11:49:43 -0400 (Tue, 16 Apr 2019).

Package 838/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lmdme 1.24.0
Cristobal Fresno
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/lmdme
Branch: RELEASE_3_8
Last Commit: 4ded3a9
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: lmdme
Version: 1.24.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:lmdme.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings lmdme_1.24.0.tar.gz
StartedAt: 2019-04-16 01:01:02 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:01:52 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 50.3 seconds
RetCode: 0
Status:  OK 
CheckDir: lmdme.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:lmdme.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings lmdme_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/lmdme.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.24.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
lmdme-printshow   5.724  0.272   3.033
lmdme-permutation 4.776  0.640   3.634
* 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-3.8-bioc/meat/lmdme.Rcheck/00check.log’
for details.



Installation output

lmdme.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL lmdme
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘lmdme’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘p.adjust’ in package ‘lmdme’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lmdme)

Tests output


Example timings

lmdme.Rcheck/lmdme-Ex.timings

nameusersystemelapsed
lmdme-biplot2.6200.0842.770
lmdme-decomposition1.9960.0082.007
lmdme-getters3.1840.0203.209
lmdme-leverage2.8640.0282.898
lmdme-lmdme2.8240.0322.861
lmdme-loadingplot2.3480.0402.390
lmdme-padjust3.0920.0403.138
lmdme-permutation4.7760.6403.634
lmdme-printshow5.7240.2723.033
lmdme-screeplot2.3920.0362.434