BioC 3.2: CHECK report for qcmetrics on oaxaca

Package: qcmetrics

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qcmetrics_1.8.0.tar.gz

StartedAt: 2015-10-27 06:50:24 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:51:43 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 78.7 seconds

RetCode: 0

Status:  OK

CheckDir: qcmetrics.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qcmetrics_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/qcmetrics.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qcmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qcmetrics’ version ‘1.8.0’
* 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 ‘qcmetrics’ can be installed ... [5s/5s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘affy’ ‘ggplot2’ ‘yaqcaffy’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
n15qc: no visible global function definition for ‘fvarLabels’
n15qc: no visible global function definition for ‘fData’
n15qc : <anonymous>: no visible global function definition for ‘ggplot’
n15qc : <anonymous>: no visible global function definition for ‘aes’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_jitter’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_boxplot’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_hline’
n15qc : <anonymous>: no visible global function definition for ‘labs’
n15qc: no visible global function definition for ‘fData<-’
n15qc: no visible global function definition for ‘combineFeatures’
n15qc: no visible global function definition for ‘exprs’
n15qc: no visible global function definition for ‘fileNames’
n15qc: no visible global function definition for ‘experimentData’
rnadeg: no visible global function definition for ‘ReadAffy’
rnadeg: no visible global function definition for ‘AffyRNAdeg’
rnadeg : <anonymous>: no visible global function definition for
  ‘plotAffyRNAdeg’
rnadeg: no visible global function definition for ‘yaqc’
* 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 ... [11s/12s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
qcReport-methods 4.339  0.537   5.575
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/qcmetrics.Rcheck/00check.log’
for details.

* installing *source* package ‘qcmetrics’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘qcmetrics’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘qcmetrics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qcmetrics)

name	user	system	elapsed
QcMetadata-class	0.003	0.000	0.004
QcMetric-class	0.016	0.002	0.018
QcMetrics-class	0.046	0.003	0.050
psm	3.660	0.094	3.757
qcReport-methods	4.339	0.537	5.575