BioC 3.4: CHECK report for IHW on morelia

Package: IHW

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IHW_1.1.3.tar.gz

StartedAt: 2016-09-20 08:04:58 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:05:39 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 40.3 seconds

RetCode: 0

Status:  OK

CheckDir: IHW.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 IHW_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/IHW.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 ‘IHW/DESCRIPTION’ ... OK
* this is package ‘IHW’ version ‘1.1.3’
* 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 ‘IHW’ 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
filter_pvals_for_optim: no visible global function definition for
  ‘p.adjust’
groups_by_filter: no visible global function definition for ‘runif’
ihw.DESeqResults: no visible global function definition for ‘mcols’
ihw.DESeqResults: no visible global function definition for ‘mcols<-’
ihw.DESeqResults: no visible global function definition for ‘metadata’
ihw.DESeqResults: no visible global function definition for
  ‘metadata<-’
ihw.default: no visible global function definition for ‘runif’
ihw.default: no visible global function definition for ‘p.adjust’
ihw_convex: no visible global function definition for ‘gurobi’
ihw_internal: no visible global function definition for ‘p.adjust’
ihw_milp: no visible global function definition for ‘str’
ihw_milp: no visible global function definition for ‘gurobi’
plot_decisionboundary: no visible binding for global variable ‘stratum’
plot_decisionboundary: no visible binding for global variable
  ‘covariate’
plot_decisionboundary: no visible binding for global variable ‘pvalue’
plot_decisionboundary: no visible binding for global variable ‘fold’
thresholds_ihwResult: no visible global function definition for
  ‘na.exclude’
thresholds,ihwResult: no visible global function definition for
  ‘na.exclude’
Undefined global functions or variables:
  covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude
  p.adjust pvalue runif str stratum
Consider adding
  importFrom("stats", "na.exclude", "p.adjust", "runif")
  importFrom("utils", "str")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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/IHW.Rcheck/00check.log’
for details.

* installing *source* package ‘IHW’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘weights’ from package ‘stats’ in package ‘IHW’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘IHW’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘IHW’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IHW)

name	user	system	elapsed
get_bh_threshold	0.002	0.000	0.002
groups_by_filter	0.002	0.000	0.002
ihw.DESeqResults	0.001	0.000	0.000
ihw.default	4.545	0.105	4.735
ihwResult-class	2.203	0.049	2.252
plot-ihwResult-method	2.591	0.061	2.653