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CHECK report for flowCyBar on tokay1

This page was generated on 2018-04-12 13:24:04 -0400 (Thu, 12 Apr 2018).

Package 478/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCyBar 1.14.0
Joachim Schumann
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/flowCyBar
Branch: RELEASE_3_6
Last Commit: c0c0a52
Last Changed Date: 2017-10-30 12:40:13 -0400 (Mon, 30 Oct 2017)
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
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowCyBar
Version: 1.14.0
Command: rm -rf flowCyBar.buildbin-libdir flowCyBar.Rcheck && mkdir flowCyBar.buildbin-libdir flowCyBar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCyBar.buildbin-libdir flowCyBar_1.14.0.tar.gz >flowCyBar.Rcheck\00install.out 2>&1 && cp flowCyBar.Rcheck\00install.out flowCyBar-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowCyBar.buildbin-libdir --install="check:flowCyBar-install.out" --force-multiarch --no-vignettes --timings flowCyBar_1.14.0.tar.gz
StartedAt: 2018-04-12 00:00:17 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:01:29 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 72.0 seconds
RetCode: 0
Status:  OK  
CheckDir: flowCyBar.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf flowCyBar.buildbin-libdir flowCyBar.Rcheck && mkdir flowCyBar.buildbin-libdir flowCyBar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCyBar.buildbin-libdir flowCyBar_1.14.0.tar.gz >flowCyBar.Rcheck\00install.out 2>&1 && cp flowCyBar.Rcheck\00install.out flowCyBar-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowCyBar.buildbin-libdir --install="check:flowCyBar-install.out" --force-multiarch --no-vignettes --timings flowCyBar_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowCyBar.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowCyBar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowCyBar' version '1.14.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowCyBar.Rcheck/00check.log'
for details.

Installation output

flowCyBar.Rcheck/00install.out


install for i386

* installing *source* package 'flowCyBar' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'flowCyBar'
    finding HTML links ... done
    Abiotic_data_sample                     html  
    Cell_number_sample                      html  
    Corr_data_sample                        html  
    correlation                             html  
    cybar_plot                              html  
    flowCyBar-package                       html  
    nmds                                    html  
    normalize                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowCyBar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCyBar' as flowCyBar_1.14.0.zip
* DONE (flowCyBar)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

flowCyBar.Rcheck/examples_i386/flowCyBar-Ex.timings

nameusersystemelapsed
correlation2.250.022.26
cybar_plot0.200.030.24
nmds0.890.031.00
normalize0.030.000.04

flowCyBar.Rcheck/examples_x64/flowCyBar-Ex.timings

nameusersystemelapsed
correlation2.980.033.02
cybar_plot0.260.000.27
nmds1.770.001.81
normalize0.060.000.06