BioC 3.5: CHECK report for pcaExplorer on toluca2

Package: pcaExplorer

Version: 2.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pcaExplorer_2.1.4.tar.gz

StartedAt: 2017-04-23 07:48:40 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:55:18 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 397.8 seconds

RetCode: 0

Status:  OK

CheckDir: pcaExplorer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pcaExplorer_2.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pcaExplorer’ version ‘2.1.4’
* 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 ‘pcaExplorer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
* 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 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
pcaExplorer: no visible binding for '<<-' assignment to
  ‘pcaexplorer_env’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘airway’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘pcaexplorer_env’
Undefined global functions or variables:
  airway pcaexplorer_env
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
distro_expr 5.423  0.027   5.501
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
correlatePCs	4.312	0.062	4.408
distro_expr	5.423	0.027	5.501
geneprofiler	2.537	0.016	2.564
genespca	4.680	0.019	4.730
get_annotation	3.203	0.083	3.310
get_annotation_orgdb	3.268	0.070	3.363
hi_loadings	2.173	0.011	2.199
limmaquickpca2go	2.429	0.068	2.506
makeExampleDESeqDataSet_multifac	0.139	0.000	0.140
pair_corr	1.932	0.074	2.017
pca2go	2.014	0.073	2.116
pcaExplorer	2.451	0.082	2.566
pcaplot	3.207	0.028	3.255
pcaplot3d	2.487	0.019	2.531
pcascree	2.818	0.010	2.842
plotPCcorrs	2.541	0.014	2.565
topGOtable	1.936	0.069	2.019