BioC 3.4: CHECK report for gespeR on zin1

Package: gespeR

Version: 1.5.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.5.2.tar.gz

StartedAt: 2016-09-20 07:14:50 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:18:10 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 199.9 seconds

RetCode: 0

Status:  OK

CheckDir: gespeR.Rcheck

Warnings: 0

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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_1.5.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/gespeR.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 ‘gespeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gespeR’ version ‘1.5.2’
* 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 ... OK
* 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 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
gespeR-package    5.084  0.228  47.950
gespeR-class      0.204  0.032  10.753
stability-methods 0.120  0.016  10.529
* 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 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
Creating a generic function for ‘as.data.frame’ from package ‘base’ in package ‘gespeR’
** 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	0.015
TargetRelations-class	0.008	0.000	0.008
annotate.gsp-methods	0.120	0.004	0.124
as.data.frame-Phenotypes-method	0.024	0.000	0.023
c-Phenotypes-method	0.020	0.000	0.021
concordance	0.404	0.004	0.409
gespeR-class	0.204	0.032	10.753
gespeR-package	5.084	0.228	47.950
gspssp-methods	0.128	0.000	0.129
join-methods	0.012	0.000	0.014
lasso.rand	0.008	0.000	0.005
na.rem-methods	0.016	0.000	0.016
path-methods	0.008	0.000	0.006
rbo	0.000	0.000	0.002
scores-methods	0.116	0.004	0.121
simData	0.012	0.000	0.012
stability-methods	0.120	0.016	10.529
stabilityfits	0.112	0.012	0.125
target-relations-methods	0.116	0.012	0.127
trmatrix-methods	0.112	0.008	0.123
values-methods	0.016	0.004	0.022