BioC 3.4: CHECK report for dcGSA on morelia

Package: dcGSA

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dcGSA_1.2.0.tar.gz

StartedAt: 2017-04-15 00:50:43 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:51:35 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 52.0 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/dcGSA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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 ‘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-3.4-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	0.122	0.001	0.123
dcGSA	0.862	0.023	0.886
dcGSAtest	0.001	0.001	0.001
readGMT	0.003	0.000	0.003