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 flowStats on tokay2


To the developers/maintainers of the flowStats package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowStats.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 672/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 4.6.0  (landing page)
Greg Finak , Mike Jiang , Jake Wagner
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/flowStats
git_branch: RELEASE_3_14
git_last_commit: afc7826
git_last_commit_date: 2021-10-26 11:53:51 -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: flowStats
Version: 4.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowStats_4.6.0.tar.gz
StartedAt: 2022-01-20 20:00:16 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:06:31 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 375.3 seconds
RetCode: 0
Status:   OK  
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowStats_4.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowStats.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 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '4.6.0'
* 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 whether package 'flowStats' can be installed ... OK
* 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
* 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
Missing object imported by a ':::' call: 'flowWorkspace:::.isBooleanGate.graphNEL'
Unexported objects imported by ':::' calls:
  'flowCore:::checkClass' 'flowCore:::copyFlowSet'
  'flowCore:::findTimeChannel' 'flowCore:::inPolygon'
  'flowViz:::evalError' 'flowViz:::plotType'
  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
.plotGPAprocess: no visible binding for global variable 'whichS'
.plotGPAprocess: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'bogus'
.usingSVD: no visible binding for global variable 'params'
density1d_simple: no visible binding for global variable 'y'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
Undefined global functions or variables:
  bogus cluster group hasPeak params whichS y
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
warpSet  13.54   0.64   14.17
plotBins  1.58   0.05    8.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
warpSet 13.42   0.18   13.61
* 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 ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowStats.Rcheck/00check.log'
for details.



Installation output

flowStats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowStats_4.6.0.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_4.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowStats_4.6.0.zip && rm flowStats_4.6.0.tar.gz flowStats_4.6.0.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
  0 1520k    0  1137    0     0  14109      0  0:01:50 --:--:--  0:01:50 14037
100 1520k  100 1520k    0     0  2343k      0 --:--:-- --:--:-- --:--:-- 2342k

install for i386

* installing *source* package 'flowStats' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowStats'
    finding HTML links ... done
    BackGating                              html  
    ITN                                     html  
    addName-methods                         html  
    autoGate                                html  
    binByRef                                html  
    calcPBChiSquare                         html  
    calcPearsonChi                          html  
    curv1Filter-class                       html  
    finding level-2 HTML links ... done

    curv2Filter-class                       html  
    curvPeaks                               html  
    density1d                               html  
    fdPar                                   html  
    flowStats-package                       html  
    gate_singlet                            html  
    gaussNorm                               html  
    gpaSet                                  html  
    iProcrustes                             html  
    idFeaturesByBackgating                  html  
    landmarkMatrix                          html  
    lymphGate                               html  
    norm2Filter-class                       html  
    normQA                                  html  
    normalize                               html  
    overton_like                            html  
    plotBins                                html  
    proBin                                  html  
    quadrantGate                            html  
    rangeGate                               html  
    spillover-flowSet                       html  
    spillover_match-flowSet                 html  
    spillover_ng-flowSet                    html  
    warpSet                                 html  
** 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

install for x64

* installing *source* package 'flowStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowStats' as flowStats_4.6.0.zip
* DONE (flowStats)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'flowStats' successfully unpacked and MD5 sums checked

Tests output

flowStats.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(flowStats)
> 
> test_check("flowStats")

Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
  14.76    0.90   42.71 

flowStats.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(flowStats)
> 
> test_check("flowStats")

Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
  15.04    1.07   29.90 

Example timings

flowStats.Rcheck/examples_i386/flowStats-Ex.timings

nameusersystemelapsed
autoGate2.110.112.22
binByRef1.140.031.17
calcPBChiSquare0.850.030.87
calcPearsonChi0.860.100.95
curv1Filter-class0.260.000.27
curv2Filter-class1.470.201.67
curvPeaks0.740.060.80
density1d3.20.13.3
gate_singlet000
gaussNorm4.270.234.50
gpaSet2.560.032.59
iProcrustes0.080.000.08
idFeaturesByBackgating0.610.050.65
landmarkMatrix0.730.010.75
lymphGate2.480.022.50
norm2Filter-class0.130.000.13
normalize000
overton_like0.010.000.01
plotBins1.580.058.16
proBin0.960.000.95
quadrantGate000
rangeGate3.060.113.18
warpSet13.54 0.6414.17

flowStats.Rcheck/examples_x64/flowStats-Ex.timings

nameusersystemelapsed
autoGate2.050.042.09
binByRef0.950.071.02
calcPBChiSquare0.610.040.66
calcPearsonChi0.720.030.75
curv1Filter-class0.280.020.29
curv2Filter-class1.500.141.64
curvPeaks0.560.050.61
density1d3.130.113.24
gate_singlet000
gaussNorm4.540.214.76
gpaSet3.050.053.10
iProcrustes0.080.020.09
idFeaturesByBackgating0.750.010.77
landmarkMatrix0.610.050.65
lymphGate2.400.092.50
norm2Filter-class0.110.000.11
normalize000
overton_like0.020.000.02
plotBins1.000.031.33
proBin0.730.020.75
quadrantGate000
rangeGate2.880.052.92
warpSet13.42 0.1813.61