Multiple platform build/check report for BioC 3.14 - CHECK results for flowStats on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

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: 2022-04-12 19:49:01 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 19:54:54 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 352.6 seconds

RetCode: 0

Status: OK

CheckDir: flowStats.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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 4.1.3 (2022-03-10)
* 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 13.62    0.5   14.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
warpSet 13.72   0.59   14.32
* 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.

##############################################################################
##############################################################################
###
### 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
 37 1520k   37  562k    0     0   940k      0  0:00:01 --:--:--  0:00:01  941k
100 1520k  100 1520k    0     0  1314k      0  0:00:01  0:00:01 --:--:-- 1315k

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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  12.70    1.15   35.31


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  14.73    0.68   16.21

name	user	system	elapsed
autoGate	1.74	0.11	1.84
binByRef	1.13	0.04	1.17
calcPBChiSquare	0.83	0.02	0.84
calcPearsonChi	0.89	0.03	0.92
curv1Filter-class	0.23	0.02	0.25
curv2Filter-class	1.39	0.23	1.62
curvPeaks	0.70	0.02	0.72
density1d	2.85	0.11	2.95
gate_singlet	0	0	0
gaussNorm	4.23	0.22	4.46
gpaSet	2.52	0.04	2.56
iProcrustes	0.10	0.00	0.09
idFeaturesByBackgating	0.65	0.03	0.69
landmarkMatrix	1.22	0.07	1.28
lymphGate	2.50	0.03	2.53
norm2Filter-class	0.13	0.00	0.12
normalize	0	0	0
overton_like	0	0	0
plotBins	1.44	0.06	1.50
proBin	0.71	0.05	0.77
quadrantGate	0	0	0
rangeGate	2.79	0.06	2.84
warpSet	13.62	0.50	14.13

name	user	system	elapsed
autoGate	2.03	0.05	2.08
binByRef	0.93	0.08	1.00
calcPBChiSquare	0.87	0.05	0.92
calcPearsonChi	0.77	0.03	0.80
curv1Filter-class	0.29	0.02	0.31
curv2Filter-class	1.67	0.03	1.70
curvPeaks	0.55	0.01	0.58
density1d	2.95	0.05	3.00
gate_singlet	0	0	0
gaussNorm	4.35	0.17	4.51
gpaSet	3.08	0.05	3.13
iProcrustes	0.11	0.00	0.11
idFeaturesByBackgating	0.76	0.01	0.78
landmarkMatrix	0.67	0.05	0.72
lymphGate	3.05	0.08	3.13
norm2Filter-class	0.14	0.00	0.14
normalize	0	0	0
overton_like	0	0	0
plotBins	0.91	0.10	3.00
proBin	0.62	0.01	0.64
quadrantGate	0	0	0
rangeGate	3.24	0.07	3.29
warpSet	13.72	0.59	14.32

CHECK results for flowStats on tokay2

Summary

Command output

Installation output

Tests output

Example timings