BioC 3.3: CHECK report for dcGSA on oaxaca

Package: dcGSA

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dcGSA_1.0.1.tar.gz

StartedAt: 2016-10-13 00:46:16 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:47:00 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 43.9 seconds

RetCode: 0

Status:  OK

CheckDir: dcGSA.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 dcGSA_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/dcGSA.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 ‘dcGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dcGSA’ version ‘1.0.1’
* 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 ‘dcGSA’ can be installed ... OK
* checking installed package size ... OK
* checking package 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
dcGSA: no visible global function definition for ‘model.matrix’
dcGSA: no visible global function definition for ‘contrasts’
dcGSA: no visible global function definition for ‘dist’
dcGSA : <anonymous>: no visible global function definition for ‘dist’
dcGSA: no visible binding for global variable ‘sd’
readGMT: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  contrasts dist model.matrix read.table sd
Consider adding
  importFrom("stats", "contrasts", "dist", "model.matrix", "sd")
  importFrom("utils", "read.table")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/dcGSA.Rcheck/00check.log’
for details.

* installing *source* package ‘dcGSA’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dcGSA)

name	user	system	elapsed
LDcov	0.018	0.000	0.019
dcGSA	1.029	0.026	1.056
dcGSAtest	0.002	0.000	0.002
readGMT	0.004	0.000	0.004