BioC 3.4: CHECK report for gespeR on morelia

Package: gespeR

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gespeR_1.5.2.tar.gz

StartedAt: 2016-09-20 07:18:51 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:22:00 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 189.1 seconds

RetCode: 0

Status:  OK

CheckDir: gespeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gespeR_1.5.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/gespeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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    5.877  0.249  36.553
gespeR-class      0.405  0.011   8.223
stability-methods 0.096  0.009   8.441
* 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
  ‘/Users/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	0.02	0.00	0.02
TargetRelations-class	0.009	0.001	0.009
annotate.gsp-methods	0.116	0.005	0.120
as.data.frame-Phenotypes-method	0.021	0.000	0.022
c-Phenotypes-method	0.023	0.001	0.023
concordance	0.365	0.012	0.378
gespeR-class	0.405	0.011	8.223
gespeR-package	5.877	0.249	36.553
gspssp-methods	0.157	0.010	0.167
join-methods	0.023	0.001	0.024
lasso.rand	0.006	0.001	0.006
na.rem-methods	0.02	0.00	0.02
path-methods	0.005	0.000	0.004
rbo	0.001	0.000	0.002
scores-methods	0.106	0.006	0.111
simData	0.012	0.000	0.012
stability-methods	0.096	0.009	8.441
stabilityfits	0.127	0.007	0.134
target-relations-methods	0.137	0.007	0.143
trmatrix-methods	0.101	0.007	0.108
values-methods	0.022	0.005	0.027