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CHECK report for flowCyBar on malbec2

This page was generated on 2019-04-09 11:38:16 -0400 (Tue, 09 Apr 2019).

Package 555/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCyBar 1.19.1
Joachim Schumann
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/flowCyBar
Branch: master
Last Commit: 16647d4
Last Changed Date: 2019-01-04 13:32:04 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: flowCyBar
Version: 1.19.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowCyBar.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowCyBar_1.19.1.tar.gz
StartedAt: 2019-04-09 00:31:35 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:32:30 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 55.0 seconds
RetCode: 0
Status:  OK 
CheckDir: flowCyBar.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowCyBar.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowCyBar_1.19.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flowCyBar.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.19.1’
* 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 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/flowCyBar.Rcheck/00check.log’
for details.



Installation output

flowCyBar.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL flowCyBar
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘flowCyBar’ ...
files ‘build/vignette.rds’, ‘inst/doc/flowCyBar-manual.R’, ‘inst/doc/flowCyBar-manual.Rnw’, ‘inst/doc/flowCyBar-manual.bib’, ‘inst/doc/flowCyBar-manual.pdf’ are missing
files ‘DESCRIPTION’, ‘R/correlation.R’, ‘R/cybar_plot.R’, ‘R/nmds.R’, ‘R/normalize.R’, ‘man/correlation.Rd’, ‘man/cybar_plot.Rd’, ‘man/flowCyBar-package.Rd’, ‘man/nmds.Rd’, ‘man/normalize.Rd’, ‘vignettes/flowCyBar-manual.Rnw’ have the wrong MD5 checksums
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowCyBar)

Tests output


Example timings

flowCyBar.Rcheck/flowCyBar-Ex.timings

nameusersystemelapsed
correlation3.0170.0123.028
cybar_plot0.3290.0000.328
nmds0.8020.0080.813
normalize0.0480.0000.047