Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:20 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for flowViz on tokay2


To the developers/maintainers of the flowViz package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowViz.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 676/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowViz 1.58.0  (landing page)
Mike Jiang , Jake Wagner
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/flowViz
git_branch: RELEASE_3_14
git_last_commit: c9fba2a
git_last_commit_date: 2021-10-26 11:50:34 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowViz
Version: 1.58.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowViz_1.58.0.tar.gz
StartedAt: 2022-01-20 20:01:10 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:04:59 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 229.5 seconds
RetCode: 0
Status:   OK  
CheckDir: flowViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowViz_1.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowViz.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.58.0'
* 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 ... 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
* 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:
  '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
.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'
densityplot,formula-ncdfFlowList: no visible global function definition
  for 'selectMethod'
densityplot,formula-view: no visible global function definition for
  'Data'
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'
histogram,formula-ncdfFlowList: no visible global function definition
  for 'selectMethod'
xyplot,formula-gateView: no visible global function definition for
  'action'
xyplot,formula-gateView: no visible global function definition for
  'Data'
xyplot,formula-gateView: no visible global function definition for
  'parent'
xyplot,formula-ncdfFlowList: no visible global function definition for
  'selectMethod'
xyplot,formula-view: no visible global function definition for 'Data'
xyplot,view-missing: no visible global function definition for 'Data'
Undefined global functions or variables:
  Data action as.formula contourLines densCols extends fd filterResult
  parent parms rainbow rl selectMethod strict
Consider adding
  importFrom("grDevices", "contourLines", "densCols", "rainbow")
  importFrom("methods", "extends", "selectMethod")
  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:150-152: 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 (user + system) or elapsed time > 5s
                 user system elapsed
densityplot     10.98   0.48   11.47
splom           11.10   0.18   11.29
xyplot           9.69   0.19    9.88
lattice-methods  7.90   0.24    8.13
timeLinePlot     6.00   0.08    6.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
splom           9.95   0.18   16.21
densityplot     9.75   0.32   10.06
xyplot          9.19   0.24    9.42
lattice-methods 7.60   0.25    7.84
timeLinePlot    5.82   0.08    5.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowViz.Rcheck/00check.log'
for details.



Installation output

flowViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowViz_1.58.0.tar.gz && rm -rf flowViz.buildbin-libdir && mkdir flowViz.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowViz.buildbin-libdir flowViz_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowViz_1.58.0.zip && rm flowViz_1.58.0.tar.gz flowViz_1.58.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 27  806k   27  221k    0     0   853k      0 --:--:-- --:--:-- --:--:--  854k
100  806k  100  806k    0     0  1689k      0 --:--:-- --:--:-- --:--:-- 1691k

install for i386

* installing *source* package 'flowViz' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'densityplot' with signature 'x="formula",data="view"': no definition for class "view"
in method for 'densityplot' with signature 'x="formula",data="ncdfFlowSet"': no definition for class "ncdfFlowSet"
in method for 'densityplot' with signature 'x="formula",data="ncdfFlowList"': no definition for class "ncdfFlowList"
in method for 'histogram' with signature 'x="formula",data="ncdfFlowSet"': no definition for class "ncdfFlowSet"
in method for 'histogram' with signature 'x="formula",data="ncdfFlowList"': no definition for class "ncdfFlowList"
in method for 'glines' with signature 'x="norm2Filter",data="ANY"': no definition for class "norm2Filter"
in method for 'glines' with signature 'x="norm2Filter",data="logicalFilterResult"': no definition for class "norm2Filter"
in method for 'glines' with signature 'x="norm2Filter",data="flowFrame"': no definition for class "norm2Filter"
in method for 'glpoints' with signature 'x="norm2Filter",data="flowFrame",channels="character"': no definition for class "norm2Filter"
in method for 'glpolygon' with signature 'x="norm2Filter",data="ANY"': no definition for class "norm2Filter"
in method for 'glpolygon' with signature 'x="norm2Filter",data="logicalFilterResult"': no definition for class "norm2Filter"
in method for 'glpolygon' with signature 'x="norm2Filter",data="flowFrame"': no definition for class "norm2Filter"
in method for 'gpoints' with signature 'x="norm2Filter",data="flowFrame",channels="character"': no definition for class "norm2Filter"
in method for 'gpolygon' with signature 'x="norm2Filter",data="ANY"': no definition for class "norm2Filter"
in method for 'gpolygon' with signature 'x="norm2Filter",data="logicalFilterResult"': no definition for class "norm2Filter"
in method for 'gpolygon' with signature 'x="norm2Filter",data="flowFrame"': no definition for class "norm2Filter"
in method for 'xyplot' with signature 'x="formula",data="view"': no definition for class "view"
in method for 'xyplot' with signature 'x="view",data="missing"': no definition for class "view"
in method for 'xyplot' with signature 'x="formula",data="gateView"': no definition for class "gateView"
in method for 'xyplot' with signature 'x="formula",data="ncdfFlowSet"': no definition for class "ncdfFlowSet"
in method for 'xyplot' with signature 'x="formula",data="ncdfFlowList"': no definition for class "ncdfFlowList"
** help
*** installing help indices
  converting help for package 'flowViz'
    finding HTML links ... done
    addName-methods                         html  
    contour-methods                         html  
    densityplot                             html  
    dot-process_flowFrame_overlay           html  
    dot-process_overlay_flowSet             html  
    ecdfplot                                html  
    flowPlot                                html  
    flowViz-package                         html  
    flowViz.par.get                         html  
    glines-methods                          html  
    glpoints-methods                        html  
    glpolygon-methods                       html  
    gpoints-methods                         html  
    gpolygon-methods                        html  
    lattice-methods                         html  
    plot                                    html  
    splom                                   html  
    timeLinePlot                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/flowViz.buildbin-libdir/00LOCK-flowViz/00new/flowViz/help/timelineplot.html
    xyplot                                  html  
** 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_1.58.0.zip
* DONE (flowViz)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'flowViz' successfully unpacked and MD5 sums checked

Tests output

flowViz.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowViz)
Loading required package: flowCore
Loading required package: lattice
> 
> test_check("flowViz")
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
   7.01    0.39    7.37 

flowViz.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowViz)
Loading required package: flowCore
Loading required package: lattice
> 
> test_check("flowViz")
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
   6.78    0.28    7.04 

Example timings

flowViz.Rcheck/examples_i386/flowViz-Ex.timings

nameusersystemelapsed
contour-methods1.300.111.41
densityplot10.98 0.4811.47
ecdfplot4.050.094.14
flowPlot0.910.040.94
flowViz-package000
flowViz.par.get2.430.042.48
lattice-methods7.900.248.13
splom11.10 0.1811.29
timeLinePlot6.000.086.08
xyplot9.690.199.88

flowViz.Rcheck/examples_x64/flowViz-Ex.timings

nameusersystemelapsed
contour-methods1.270.111.37
densityplot 9.75 0.3210.06
ecdfplot3.350.073.42
flowPlot0.680.040.72
flowViz-package000
flowViz.par.get1.500.031.53
lattice-methods7.600.257.84
splom 9.95 0.1816.21
timeLinePlot5.820.085.91
xyplot9.190.249.42