BioC 3.3: CHECK report for metabomxtr on zin2

Package: metabomxtr

Version: 1.6.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metabomxtr_1.6.0.tar.gz

StartedAt: 2016-10-13 04:06:41 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:07:33 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 52.1 seconds

RetCode: 0

Status:  OK

CheckDir: metabomxtr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metabomxtr_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/metabomxtr.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 ‘metabomxtr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabomxtr’ version ‘1.6.0’
* 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 ‘metabomxtr’ 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
mixnorm: no visible global function definition for ‘as.formula’
mxtrmod : <anonymous>: no visible global function definition for ‘coef’
mxtrmodLL: no visible global function definition for ‘dnorm’
mxtrmodLL: no visible global function definition for ‘pnorm’
mxtrmodLRT: no visible global function definition for ‘pchisq’
mxtrmodstart: no visible global function definition for ‘sd’
xdesign,ExpressionSet: no visible binding for global variable ‘na.pass’
xdesign,ExpressionSet: no visible global function definition for
  ‘model.matrix’
xdesign,ExpressionSet: no visible global function definition for
  ‘formula’
xdesign,data.frame: no visible binding for global variable ‘na.pass’
xdesign,data.frame: no visible global function definition for
  ‘model.matrix’
xdesign,data.frame: no visible global function definition for ‘formula’
xdesign,matrix: no visible binding for global variable ‘na.pass’
xdesign,matrix: no visible global function definition for
  ‘model.matrix’
xdesign,matrix: no visible global function definition for ‘formula’
zdesign,ExpressionSet: no visible binding for global variable ‘na.pass’
zdesign,ExpressionSet: no visible global function definition for
  ‘model.matrix’
zdesign,ExpressionSet: no visible global function definition for
  ‘formula’
zdesign,data.frame: no visible binding for global variable ‘na.pass’
zdesign,data.frame: no visible global function definition for
  ‘model.matrix’
zdesign,data.frame: no visible global function definition for ‘formula’
zdesign,matrix: no visible binding for global variable ‘na.pass’
zdesign,matrix: no visible global function definition for
  ‘model.matrix’
zdesign,matrix: no visible global function definition for ‘formula’
Undefined global functions or variables:
  as.formula coef dnorm formula model.matrix na.pass pchisq pnorm sd
Consider adding
  importFrom("stats", "as.formula", "coef", "dnorm", "formula",
             "model.matrix", "na.pass", "pchisq", "pnorm", "sd")
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
* 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-3.3-bioc/meat/metabomxtr.Rcheck/00check.log’
for details.

* installing *source* package ‘metabomxtr’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metabomxtr)

name	user	system	elapsed
metabomxtr-package	1.313	0.001	1.313
mixnorm	0.579	0.000	0.581
mxtrmod	2.296	0.039	2.339
mxtrmodLL	0.005	0.000	0.004
mxtrmodLRT	0.829	0.008	0.839
mxtrmodstart	0.004	0.000	0.004