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BioC 3.4: CHECK report for flowCyBar on morelia

This page was generated on 2017-04-15 16:25:25 -0400 (Sat, 15 Apr 2017).

Package 430/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCyBar 1.10.0
Joachim Schumann
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/flowCyBar
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowCyBar
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowCyBar_1.10.0.tar.gz
StartedAt: 2017-04-15 02:08:44 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 02:09:39 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 54.1 seconds
RetCode: 0
Status:  OK 
CheckDir: flowCyBar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowCyBar_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowCyBar.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCyBar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowCyBar’ version ‘1.10.0’
* package encoding: UTF-8
* 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 ‘flowCyBar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
correlation,data.frame : <anonymous>: no visible global function
  definition for ‘as.dist’
correlation,data.frame : est: no visible global function definition for
  ‘cor.test’
correlation,data.frame : pval: no visible global function definition
  for ‘cor.test’
correlation,matrix : <anonymous>: no visible global function definition
  for ‘as.dist’
correlation,matrix : est: no visible global function definition for
  ‘cor.test’
correlation,matrix : pval: no visible global function definition for
  ‘cor.test’
cybar_plot,data.frame-data.frame: no visible global function definition
  for ‘layout’
cybar_plot,data.frame-data.frame: no visible global function definition
  for ‘par’
cybar_plot,data.frame-data.frame: no visible global function definition
  for ‘boxplot’
cybar_plot,data.frame-matrix: no visible global function definition for
  ‘layout’
cybar_plot,data.frame-matrix: no visible global function definition for
  ‘par’
cybar_plot,data.frame-matrix: no visible global function definition for
  ‘boxplot’
cybar_plot,matrix-data.frame: no visible global function definition for
  ‘layout’
cybar_plot,matrix-data.frame: no visible global function definition for
  ‘par’
cybar_plot,matrix-data.frame: no visible global function definition for
  ‘boxplot’
cybar_plot,matrix-matrix: no visible global function definition for
  ‘layout’
cybar_plot,matrix-matrix: no visible global function definition for
  ‘par’
cybar_plot,matrix-matrix: no visible global function definition for
  ‘boxplot’
cybar_plot,missing-data.frame: no visible global function definition
  for ‘boxplot’
cybar_plot,missing-matrix: no visible global function definition for
  ‘boxplot’
nmds,data.frame: no visible global function definition for ‘plot’
nmds,data.frame: no visible global function definition for ‘text’
nmds,data.frame: no visible global function definition for ‘points’
nmds,data.frame: no visible global function definition for ‘legend’
nmds,matrix: no visible global function definition for ‘plot’
nmds,matrix: no visible global function definition for ‘text’
nmds,matrix: no visible global function definition for ‘points’
nmds,matrix: no visible global function definition for ‘legend’
normalize,data.frame : <anonymous>: no visible global function
  definition for ‘head’
normalize,matrix : <anonymous>: no visible global function definition
  for ‘head’
Undefined global functions or variables:
  as.dist boxplot cor.test head layout legend par plot points text
Consider adding
  importFrom("graphics", "boxplot", "layout", "legend", "par", "plot",
             "points", "text")
  importFrom("stats", "as.dist", "cor.test")
  importFrom("utils", "head")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowCyBar.Rcheck/00check.log’
for details.


flowCyBar.Rcheck/00install.out:

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

flowCyBar.Rcheck/flowCyBar-Ex.timings:

nameusersystemelapsed
correlation2.8430.0192.948
cybar_plot0.2870.0060.295
nmds0.6480.0300.681
normalize0.0490.0040.053