BioC 3.4: CHECK report for affyILM on zin1

Package: affyILM

Version: 1.25.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affyILM_1.25.0.tar.gz

StartedAt: 2016-09-20 02:58:38 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:00:09 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 90.8 seconds

RetCode: 0

Status:  OK

CheckDir: affyILM.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 affyILM_1.25.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/affyILM.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 ‘affyILM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘affyILM’ 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 ‘affyILM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘gcrma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.affyILM_scale: no visible binding for global variable ‘median’
.affyILM_scale: no visible binding for global variable ‘mad’
.affyILM_scale: no visible global function definition for ‘median’
.getChipInfo: no visible global function definition for
  ‘getProbePackage’
.summarizeConcs: no visible binding for global variable ‘mad’
.summarizeConcs: no visible binding for global variable ‘median’
.summarizeMedpolish: no visible global function definition for
  ‘medpolish’
.summarizeTrMedpolish: no visible global function definition for
  ‘medpolish’
ilm: no visible global function definition for ‘getProbePackage’
plotILM,ILM: no visible global function definition for ‘median’
plotILM,ILM: no visible global function definition for ‘mad’
Undefined global functions or variables:
  getProbePackage mad median medpolish
Consider adding
  importFrom("stats", "mad", "median", "medpolish")
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 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
ilm-methods 11.88  0.712  14.507
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/affyILM.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ILM-class	0.000	0.000	0.002
ilm-methods	11.880	0.712	14.507
ilm	4.180	0.012	4.214
plotILM	2.352	0.004	2.354
plotIntens	2.100	0.024	2.123