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BioC 3.5: CHECK report for flowViz on toluca2

This page was generated on 2017-04-23 14:33:58 -0400 (Sun, 23 Apr 2017).

Package 473/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowViz 1.39.3
Mike Jiang
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowViz
Last Changed Rev: 127465 / Revision: 129046
Last Changed Date: 2017-03-16 16:11:52 -0400 (Thu, 16 Mar 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowViz
Version: 1.39.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowViz_1.39.3.tar.gz
StartedAt: 2017-04-23 03:57:38 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 04:00:02 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 144.4 seconds
RetCode: 0
Status:  OK 
CheckDir: flowViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowViz_1.39.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowViz.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowViz’ version ‘1.39.3’
* 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 ‘flowViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘lattice’
A package should be listed in only one of these fields.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘flowCore:::findTimeChannel’ ‘flowCore:::prepareSet’
  ‘lattice:::hist.constructor’ ‘lattice:::updateList’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
flowPlot,flowFrame: warning in log(xd, b = 10): partial argument match
  of 'b' to 'base'
flowPlot,flowFrame: warning in log(yd, b = 10): partial argument match
  of 'b' to 'base'
.process_overlay_flowSet : <anonymous>: no visible global function
  definition for ‘extends’
.xyplot.flowSet: no visible global function definition for ‘as.formula’
panel.densityplot.flowset.stack: no visible binding for global variable
  ‘rl’
panel.xyplot.flowframe: no visible global function definition for
  ‘densCols’
panel.xyplot.flowframe.old: no visible global function definition for
  ‘densCols’
prepanel.densityplot.flowset.stack: no visible global function
  definition for ‘extends’
contour,flowFrame: no visible global function definition for
  ‘contourLines’
flowPlot,flowFrame: no visible global function definition for ‘rainbow’
glpoints,filter-flowFrame-missing: no visible binding for global
  variable ‘parms’
glpoints,filter-flowFrame-missing: no visible binding for global
  variable ‘strict’
gpoints,quadGate-flowFrame-character: no visible binding for global
  variable ‘filterResult’
gpolygon,ellipsoidGate-character: no visible binding for global
  variable ‘fd’
Undefined global functions or variables:
  as.formula contourLines densCols extends fd filterResult parms
  rainbow rl strict
Consider adding
  importFrom("grDevices", "contourLines", "densCols", "rainbow")
  importFrom("methods", "extends")
  importFrom("stats", "as.formula")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: glines-methods.Rd:149-151: Dropping empty section ‘Methods’
prepare_Rd: timeLinePlot.Rd:72-74: Dropping empty section ‘Methods’
* 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
Examples with CPU or elapsed time > 5s
                  user system elapsed
densityplot     15.968  0.520  16.764
xyplot          12.462  0.368  12.991
splom           10.835  0.460  11.442
lattice-methods  7.637  1.179   8.907
ecdfplot         7.171  1.395   8.751
timeLinePlot     7.100  0.248   7.423
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘data.table’
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowViz.Rcheck/00check.log’
for details.


flowViz.Rcheck/00install.out:

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

flowViz.Rcheck/flowViz-Ex.timings:

nameusersystemelapsed
contour-methods1.6150.0951.723
densityplot15.968 0.52016.764
ecdfplot7.1711.3958.751
flowPlot1.1600.0691.240
flowViz-package0.0000.0000.001
flowViz.par.get1.9210.0612.029
lattice-methods7.6371.1798.907
splom10.835 0.46011.442
timeLinePlot7.1000.2487.423
xyplot12.462 0.36812.991