Back to Multiple platform build/check report for BioC 3.14
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-22 12:04:26 -0400 (Fri, 22 Oct 2021).

CHECK results for flowStats on riesling1

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 668/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 4.5.1  (landing page)
Greg Finak , Mike Jiang , Jake Wagner
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/flowStats
git_branch: master
git_last_commit: 5932e47
git_last_commit_date: 2021-07-30 14:05:12 -0400 (Fri, 30 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: flowStats
Version: 4.5.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowStats_4.5.1.tar.gz
StartedAt: 2021-10-22 01:06:12 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 01:09:38 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 205.6 seconds
RetCode: 0
Status:   OK  
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowStats_4.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/flowStats.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '4.5.1'
* 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 9.46   0.53    9.99
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
warpSet 10.2   0.18   10.39
* 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
  'D:/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_4.5.1.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_4.5.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowStats_4.5.1.zip && rm flowStats_4.5.1.tar.gz flowStats_4.5.1.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
 68 1520k   68 1045k    0     0  1745k      0 --:--:-- --:--:-- --:--:-- 1742k
100 1520k  100 1520k    0     0  2029k      0 --:--:-- --:--:-- --:--:-- 2027k

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_4.5.1.zip
* DONE (flowStats)
* installing to library 'D:/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 4.1.1 (2021-08-10) -- "Kick Things"
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 
   9.26    0.37    9.87 

flowStats.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
   9.96    0.56   10.82 

Example timings

flowStats.Rcheck/examples_i386/flowStats-Ex.timings

nameusersystemelapsed
autoGate1.520.061.57
binByRef0.750.060.82
calcPBChiSquare0.570.020.59
calcPearsonChi0.630.040.67
curv1Filter-class0.180.000.17
curv2Filter-class0.920.070.98
curvPeaks0.500.040.55
density1d2.230.062.30
gate_singlet000
gaussNorm2.990.183.15
gpaSet1.840.061.91
iProcrustes0.060.000.06
idFeaturesByBackgating0.50.00.5
landmarkMatrix0.580.000.58
lymphGate1.780.051.83
norm2Filter-class0.090.000.09
normalize000
overton_like0.020.000.02
plotBins0.780.060.84
proBin0.480.050.53
quadrantGate000
rangeGate2.030.052.08
warpSet9.460.539.99

flowStats.Rcheck/examples_x64/flowStats-Ex.timings

nameusersystemelapsed
autoGate1.490.051.53
binByRef0.720.020.74
calcPBChiSquare0.440.030.47
calcPearsonChi0.480.040.53
curv1Filter-class0.190.000.19
curv2Filter-class0.970.071.03
curvPeaks0.360.040.40
density1d2.140.082.22
gate_singlet000
gaussNorm3.020.133.14
gpaSet2.170.042.22
iProcrustes0.060.000.06
idFeaturesByBackgating0.520.020.53
landmarkMatrix0.470.020.49
lymphGate1.930.031.96
norm2Filter-class0.10.00.1
normalize000
overton_like000
plotBins0.650.030.69
proBin0.380.040.42
quadrantGate000
rangeGate2.250.072.31
warpSet10.20 0.1810.39