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BioC 3.5: CHECK report for pcaExplorer on veracruz2

This page was generated on 2017-10-18 14:34:32 -0400 (Wed, 18 Oct 2017).

Package 959/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaExplorer 2.2.1
Federico Marini
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/pcaExplorer
Branch: RELEASE_3_5
Last Commit: a36b15e
Last Changed Date: 2017-08-28 15:22:23 -0400 (Mon, 28 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pcaExplorer
Version: 2.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pcaExplorer_2.2.1.tar.gz
StartedAt: 2017-10-18 07:08:21 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 07:14:29 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 367.6 seconds
RetCode: 0
Status:  OK 
CheckDir: pcaExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pcaExplorer_2.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.2.1’
* 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
* 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.


pcaExplorer.Rcheck/00install.out:

* 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)

pcaExplorer.Rcheck/pcaExplorer-Ex.timings:

nameusersystemelapsed
correlatePCs3.7420.0693.956
distro_expr4.7870.0374.992
geneprofiler2.5180.0162.605
genespca4.2850.0614.481
get_annotation3.7600.0993.969
get_annotation_orgdb2.6840.0682.832
hi_loadings2.6030.0232.697
limmaquickpca2go2.2460.0682.376
makeExampleDESeqDataSet_multifac0.1610.0010.164
pair_corr3.2690.0783.437
pca2go2.4620.0772.607
pcaExplorer2.3810.0662.547
pcaplot2.7820.0332.911
pcaplot3d2.1250.0372.247
pcascree2.3920.0142.497
plotPCcorrs2.3640.0172.461
topGOtable1.8610.0731.982