BioC 3.4: CHECK report for gespeR on malbec1

Package: gespeR

Version: 1.6.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.6.1.tar.gz

StartedAt: 2017-04-14 22:52:49 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:56:41 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 232.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gespeR.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/gespeR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gespeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gespeR’ version ‘1.6.1’
* 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 ‘gespeR’ 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
.gespeR.cv: no visible global function definition for ‘coef’
.select.model: no visible global function definition for ‘predict’
concordance: no visible global function definition for ‘cor’
lasso.rand: no visible global function definition for ‘runif’
plot.gespeR: no visible global function definition for ‘hist’
stability.selection: no visible global function definition for ‘lm’
Phenotypes,character: no visible global function definition for
  ‘read.delim’
Undefined global functions or variables:
  coef cor hist lm predict read.delim runif
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "cor", "lm", "predict", "runif")
  importFrom("utils", "read.delim")
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 ... WARNING
Codoc mismatches from documentation object 'c,Phenotypes-method':
\S4method{c}{Phenotypes}
  Code: function(x, ...)
  Docs: function(x, ..., recursive = FALSE)
  Argument names in docs not in code:
    recursive

* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
gespeR-package    5.596  0.444  55.395
gespeR-class      0.312  0.028  12.102
stability-methods 0.128  0.040  12.062
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/gespeR.Rcheck/00check.log’
for details.

* installing *source* package ‘gespeR’ ...
** 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 (gespeR)

name	user	system	elapsed
Phenotypes-class	0.016	0.000	0.016
TargetRelations-class	0.004	0.000	0.007
annotate.gsp-methods	0.112	0.000	0.112
as.data.frame-Phenotypes-method	0.020	0.000	0.021
c-Phenotypes-method	0.02	0.00	0.02
concordance	0.688	0.004	0.696
gespeR-class	0.312	0.028	12.102
gespeR-package	5.596	0.444	55.395
gspssp-methods	0.136	0.004	0.139
join-methods	0.016	0.000	0.015
lasso.rand	0.004	0.000	0.004
na.rem-methods	0.016	0.000	0.016
path-methods	0.008	0.000	0.006
rbo	0.004	0.000	0.001
scores-methods	0.128	0.000	0.128
simData	0.012	0.000	0.012
stability-methods	0.128	0.040	12.062
stabilityfits	0.156	0.004	0.159
target-relations-methods	0.124	0.000	0.124
trmatrix-methods	0.128	0.000	0.127
values-methods	0.016	0.008	0.021