BioC 3.5: CHECK report for gespeR on malbec2

Package: gespeR

Version: 1.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.8.0.tar.gz

StartedAt: 2017-10-17 23:36:46 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:40:47 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 241.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gespeR.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/gespeR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.8.0’
* 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 ‘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 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    6.600  0.488  57.490
gespeR-class      0.888  0.084  13.549
stability-methods 0.124  0.036  12.937
* 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-3.5-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	0.017
TargetRelations-class	0.008	0.000	0.008
annotate.gsp-methods	0.152	0.000	0.151
as.data.frame-Phenotypes-method	0.064	0.008	0.074
c-Phenotypes-method	0.164	0.020	0.185
concordance	1.244	0.000	1.244
gespeR-class	0.888	0.084	13.549
gespeR-package	6.600	0.488	57.490
gspssp-methods	0.136	0.016	0.152
join-methods	0.012	0.000	0.014
lasso.rand	0.004	0.000	0.005
na.rem-methods	0.020	0.000	0.021
path-methods	0.004	0.000	0.006
rbo	0.004	0.000	0.001
scores-methods	0.120	0.012	0.132
simData	0.012	0.000	0.011
stability-methods	0.124	0.036	12.937
stabilityfits	0.140	0.016	0.154
target-relations-methods	0.116	0.004	0.121
trmatrix-methods	0.116	0.016	0.132
values-methods	0.020	0.012	0.032