BioC 3.3: CHECK report for EasyqpcR on zin2

Package: EasyqpcR

Version: 1.14.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings EasyqpcR_1.14.0.tar.gz

StartedAt: 2016-10-13 01:32:13 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:32:56 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 42.7 seconds

RetCode: 0

Status:  OK

CheckDir: EasyqpcR.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 EasyqpcR_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/EasyqpcR.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 ‘EasyqpcR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EasyqpcR’ version ‘1.14.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘gWidgetsRGtk2’
* 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 ‘EasyqpcR’ 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
badCt: no visible global function definition for ‘aggregate’
nrmData: no visible global function definition for ‘aggregate’
nrmData: no visible binding for global variable ‘sd’
slope: no visible global function definition for ‘aggregate’
slope: no visible global function definition for ‘coef’
slope: no visible global function definition for ‘lm’
slope: no visible global function definition for ‘combn’
totData: no visible global function definition for ‘aggregate’
totData: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate coef combn lm sd
Consider adding
  importFrom("stats", "aggregate", "coef", "lm", "sd")
  importFrom("utils", "combn")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘vignette_EasyqpcR.toc’
Please remove them from your package.
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/EasyqpcR.Rcheck/00check.log’
for details.

* installing *source* package ‘EasyqpcR’ ...
** R
** data
** inst
** preparing package for lazy loading
Xlib:  extension "RANDR" missing on display ":1.0".
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Xlib:  extension "RANDR" missing on display ":1.0".
* DONE (EasyqpcR)

name	user	system	elapsed
Efficiency_calculation	0.1	0.0	0.1
Gene_maximisation	0.001	0.004	0.002
Gene_maximisation_cor	0.001	0.000	0.003
badCt	0.021	0.000	0.021
calData	0.202	0.000	0.207
nrmData	0.094	0.004	0.104
qPCR_run1	0.002	0.000	0.002
qPCR_run2	0.001	0.000	0.001
qPCR_run3	0.000	0.004	0.002
slope	0.009	0.000	0.010
totData	0.460	0.012	0.479