Back to Multiple platform build/check report for BioC 3.13
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).

CHECK results for flowSpecs on tokay2

To the developers/maintainers of the flowSpecs package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowSpecs.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 662/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowSpecs 1.6.0  (landing page)
Jakob Theorell
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/flowSpecs
git_branch: RELEASE_3_13
git_last_commit: e8a3b4e
git_last_commit_date: 2021-05-19 12:46:22 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: flowSpecs
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowSpecs.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowSpecs_1.6.0.tar.gz
StartedAt: 2021-10-14 23:16:17 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:18:32 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 135.0 seconds
RetCode: 0
Status:   OK  
CheckDir: flowSpecs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowSpecs.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowSpecs_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowSpecs.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 'flowSpecs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowSpecs' version '1.6.0'
* 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 'flowSpecs' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
** running examples for arch 'x64' ... OK
* 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: OK


Installation output

flowSpecs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowSpecs_1.6.0.tar.gz && rm -rf flowSpecs.buildbin-libdir && mkdir flowSpecs.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowSpecs.buildbin-libdir flowSpecs_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowSpecs_1.6.0.zip && rm flowSpecs_1.6.0.tar.gz flowSpecs_1.6.0.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
 34 2791k   34  963k    0     0  1115k      0  0:00:02 --:--:--  0:00:02 1115k
100 2791k  100 2791k    0     0  1595k      0  0:00:01  0:00:01 --:--:-- 1596k

install for i386

* installing *source* package 'flowSpecs' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowSpecs'
    finding HTML links ... done
    arcTrans                                html  
    corrMatCreate                           html  
    correctUnmix                            html  
    flowSet2LongDf                          html  
    flowSpecs-package                       html  
    fullPanel                               html  
    newExprs-set                            html  
    oneVsAllPlot                            html  
    peakIdenti                              html  
    peakNorm                                html  
    specMat                                 html  
    specMatCalc                             html  
    specUnmix                               html  
    unmixCtrls                              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 'flowSpecs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowSpecs' as flowSpecs_1.6.0.zip
* DONE (flowSpecs)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'flowSpecs' successfully unpacked and MD5 sums checked

Tests output

flowSpecs.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(flowSpecs)
> library(flowCore)
> test_check("flowSpecs")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
   5.17    0.26    5.40 

flowSpecs.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(flowSpecs)
> library(flowCore)
> test_check("flowSpecs")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
   4.95    0.21    5.15 

Example timings

flowSpecs.Rcheck/examples_i386/flowSpecs-Ex.timings

nameusersystemelapsed
arcTrans0.240.040.28
corrMatCreate0.260.000.26
correctUnmix3.310.183.49
flowSet2LongDf0.270.030.30
oneVsAllPlot1.360.061.42
peakNorm1.030.081.11
specMatCalc3.670.013.68
specUnmix0.220.030.25

flowSpecs.Rcheck/examples_x64/flowSpecs-Ex.timings

nameusersystemelapsed
arcTrans0.250.000.25
corrMatCreate0.220.050.27
correctUnmix3.850.194.03
flowSet2LongDf0.470.040.52
oneVsAllPlot1.610.041.64
peakNorm0.830.060.89
specMatCalc4.120.014.14
specUnmix0.220.020.23