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BioC 3.6: CHECK report for flowVS on veracruz1

This page was generated on 2017-08-16 13:47:06 -0400 (Wed, 16 Aug 2017).

Package 482/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowVS 1.9.0
Ariful Azad
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowVS
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 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 [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowVS
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowVS_1.9.0.tar.gz
StartedAt: 2017-08-16 03:10:54 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:13:06 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 132.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowVS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowVS_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/flowVS.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowVS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowVS’ version ‘1.9.0’
* 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 ‘flowVS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/flowVS.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 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
bartlettTestMicro: no visible binding for global variable ‘var’
curvPeaks: no visible global function definition for ‘density’
curvPeaks: no visible global function definition for ‘quantile’
curvPeaks: no visible global function definition for ‘approxfun’
curvPeaks: no visible global function definition for ‘optimize’
densityPeaks: no visible global function definition for ‘quantile’
densityPeaks: no visible global function definition for ‘density’
densityPeaks: no visible global function definition for ‘median’
densityPeaks: no visible global function definition for ‘var’
densityPeaks: no visible global function definition for ‘colorRamp’
densityPeaks: no visible global function definition for ‘rgb’
densityPeaks: no visible global function definition for ‘polygon’
densityPeaks: no visible global function definition for ‘lines’
densityPeaks: no visible global function definition for ‘abline’
densityPeaks: no visible global function definition for ‘dev.copy2pdf’
flowVS1D: no visible global function definition for ‘median’
lymphs: no visible global function definition for ‘as.formula’
lymphs: no visible global function definition for ‘colorRampPalette’
microVS: no visible global function definition for ‘quantile’
microVS: no visible global function definition for ‘points’
optimStat: no visible global function definition for ‘optimize’
optimStat: no visible global function definition for ‘points’
peakStats1D: no visible global function definition for ‘median’
plotMeanSd : mediwind: no visible global function definition for
  ‘median’
plotMeanSd: no visible global function definition for ‘quantile’
plotMeanSd: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline approxfun as.formula colorRamp colorRampPalette density
  dev.copy2pdf lines median optimize points polygon quantile rgb var
Consider adding
  importFrom("grDevices", "colorRamp", "colorRampPalette",
             "dev.copy2pdf", "rgb")
  importFrom("graphics", "abline", "lines", "points", "polygon")
  importFrom("stats", "approxfun", "as.formula", "density", "median",
             "optimize", "quantile", "var")
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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/flowVS.Rcheck/00check.log’
for details.


flowVS.Rcheck/00install.out:

* installing *source* package ‘flowVS’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowVS)

flowVS.Rcheck/flowVS-Ex.timings:

nameusersystemelapsed
estParamFlowVS0.0300.0050.041
lymphs1.2810.0461.342
microVS4.1520.0514.583
plotMeanSd3.7710.0143.848
transFlowVS0.0300.0040.033