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CHECK report for flowViz on tokay2

This page was generated on 2019-10-16 12:20:59 -0400 (Wed, 16 Oct 2019).

Package 584/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowViz 1.48.0
Mike Jiang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/flowViz
Branch: RELEASE_3_9
Last Commit: 13d9ca5
Last Changed Date: 2019-05-02 11:53:07 -0400 (Thu, 02 May 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 [ WARNINGS ] 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

Summary

Package: flowViz
Version: 1.48.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flowViz_1.48.0.tar.gz
StartedAt: 2019-10-16 03:47:04 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:50:36 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 211.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowViz.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flowViz_1.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flowViz.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowViz' version '1.48.0'
* 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 whether package 'flowViz' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:86: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:98: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:105: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:112: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:119: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:118: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:130: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:137: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:144: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:151: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:111: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:123: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:130: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:137: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:144: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/xyplot.Rd:104: file link 'filtersList-class' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/xyplot.Rd:174: file link 'sqrt' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flowViz.Rcheck/00install.out' for details.
* 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
* 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
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  '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 : : 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' ... NOTE
Files named as vignettes but with no recognized vignette engine:
   'vignettes/densityplot_vs_histogram.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
densityplot     13.12   0.40   13.55
xyplot          11.09   0.14   11.24
splom           10.24   0.26   10.50
lattice-methods  9.81   0.41   10.22
timeLinePlot     7.17   0.08    7.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
xyplot          10.89   0.13   11.01
densityplot     10.10   0.47   10.56
splom           10.00   0.19   10.18
lattice-methods  8.63   0.53    9.16
timeLinePlot     5.86   0.06    5.93
ecdfplot         5.27   0.13    5.40
* 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: 1 WARNING, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/flowViz.Rcheck/00check.log'
for details.

Installation output

flowViz.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flowViz_1.48.0.tar.gz && rm -rf flowViz.buildbin-libdir && mkdir flowViz.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowViz.buildbin-libdir flowViz_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flowViz_1.48.0.zip && rm flowViz_1.48.0.tar.gz flowViz_1.48.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  806k  100  806k    0     0  10.8M      0 --:--:-- --:--:-- --:--:-- 12.1M

install for i386

* installing *source* package 'flowViz' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowViz'
    finding HTML links ... done
    addName-methods                         html  
    contour-methods                         html  
    densityplot                             html  
    ecdfplot                                html  
    flowPlot                                html  
    flowViz-package                         html  
    flowViz.par.get                         html  
    glines-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:86: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:98: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:105: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:112: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glines-methods.Rd:119: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
    glpoints-methods                        html  
    glpolygon-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:118: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:130: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:137: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:144: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/glpolygon-methods.Rd:151: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
    gpoints-methods                         html  
    gpolygon-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:111: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:123: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:130: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:137: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/gpolygon-methods.Rd:144: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
    lattice-methods                         html  
    plot                                    html  
    splom                                   html  
    timeLinePlot                            html  
    xyplot                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/xyplot.Rd:104: file link 'filtersList-class' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsXG0vU/R.INSTALL126019aa6165/flowViz/man/xyplot.Rd:174: file link 'sqrt' in package 'base' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
   'filters.Rmd' 
** 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

install for x64

* installing *source* package 'flowViz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowViz' as flowViz_1.48.0.zip
* DONE (flowViz)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'flowViz' successfully unpacked and MD5 sums checked

Tests output

Example timings

flowViz.Rcheck/examples_i386/flowViz-Ex.timings

nameusersystemelapsed
contour-methods1.630.051.68
densityplot13.12 0.4013.55
ecdfplot4.390.174.56
flowPlot0.920.070.98
flowViz-package000
flowViz.par.get1.220.011.25
lattice-methods 9.81 0.4110.22
splom10.24 0.2610.50
timeLinePlot7.170.087.25
xyplot11.09 0.1411.24

flowViz.Rcheck/examples_x64/flowViz-Ex.timings

nameusersystemelapsed
contour-methods1.530.031.56
densityplot10.10 0.4710.56
ecdfplot5.270.135.40
flowPlot1.620.041.67
flowViz-package0.020.000.02
flowViz.par.get2.060.072.12
lattice-methods8.630.539.16
splom10.00 0.1910.18
timeLinePlot5.860.065.93
xyplot10.89 0.1311.01