BioC 3.4: CHECK report for frma on zin1

Package: frma

Version: 1.25.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings frma_1.25.0.tar.gz

StartedAt: 2016-09-20 06:40:03 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:42:31 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 148.6 seconds

RetCode: 0

Status:  OK

CheckDir: frma.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings frma_1.25.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/frma.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 ‘frma/DESCRIPTION’ ... OK
* this is package ‘frma’ version ‘1.25.0’
* 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 ‘frma’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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
GNUSE: no visible binding for global variable ‘median’
GNUSE: no visible binding for global variable ‘quantile’
GNUSE: no visible global function definition for ‘boxplot’
barcode: no visible global function definition for ‘pnorm’
batchFit: no visible global function definition for ‘median’
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for ‘slot<-’
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for ‘slot’
randomeffects<-,frmaExpressionSet: no visible global function
  definition for ‘validObject’
residuals<-,frmaExpressionSet: no visible global function definition
  for ‘validObject’
se.exprs<-,ExpressionSet: no visible global function definition for
  ‘validObject’
se.exprs<-,frmaExpressionSet: no visible global function definition for
  ‘validObject’
weights<-,frmaExpressionSet: no visible global function definition for
  ‘validObject’
Undefined global functions or variables:
  boxplot median pnorm quantile slot slot<- validObject
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("methods", "slot", "slot<-", "validObject")
  importFrom("stats", "median", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
GNUSE   13.700  0.204  13.948
frma     9.860  0.004   9.867
barcode  9.808  0.024   9.848
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/frma.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GNUSE	13.700	0.204	13.948
barcode	9.808	0.024	9.848
frma	9.860	0.004	9.867
frmaExpressionSet-class	0.120	0.000	0.123