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

This page was generated on 2022-01-14 13:06:23 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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

CHECK results for flowDensity on tokay2


To the developers/maintainers of the flowDensity package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowDensity.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 660/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.28.0  (landing page)
Mehrnoush Malek
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/flowDensity
git_branch: RELEASE_3_14
git_last_commit: 26bbabf
git_last_commit_date: 2021-10-26 12:14:21 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowDensity
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowDensity.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowDensity_1.28.0.tar.gz
StartedAt: 2022-01-13 19:27:17 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 19:32:32 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 315.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowDensity.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowDensity.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowDensity_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowDensity.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 'flowDensity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowDensity' version '1.28.0'
* 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 'flowDensity' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowDensity.Rcheck/00install.out' for details.
* 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 ... WARNING
Rd files with duplicated alias 'flowDensity':
  'flowDensity-methods.Rd' 'flowDensity.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'flowDensity' and siglist
    'CellPopulation,ANY,logical,missing'
  generic 'flowDensity' and siglist 'GatingHierarchy,ANY,logical,ANY'
  generic 'flowDensity' and siglist 'flowFrame,ANY,logical,missing'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'flowDensity-methods':
  '\S4method{flowDensity}{CellPopulation,ANY,logical,missing}'
  '\S4method{flowDensity}{flowFrame,ANY,logical,missing}'
  '\S4method{flowDensity}{GatingHierarchy,ANY,logical,ANY}'

Undocumented arguments in documentation object 'plotDens'
  'dens.col' 'cex' 'dens.type'
Documented arguments not in \usage in documentation object 'plotDens':
  'density.type' 'density.col'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... 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
notSubFrame 0.22   0.02    5.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
notSubFrame 0.13   0.01   23.61
* 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: 4 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowDensity.Rcheck/00check.log'
for details.



Installation output

flowDensity.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowDensity_1.28.0.tar.gz && rm -rf flowDensity.buildbin-libdir && mkdir flowDensity.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowDensity.buildbin-libdir flowDensity_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowDensity_1.28.0.zip && rm flowDensity_1.28.0.tar.gz flowDensity_1.28.0.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
 40 4396k   40 1791k    0     0  3471k      0  0:00:01 --:--:--  0:00:01 3471k
100 4396k  100 4396k    0     0  4266k      0  0:00:01  0:00:01 --:--:-- 4272k

install for i386

* installing *source* package 'flowDensity' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
** help
*** installing help indices
  converting help for package 'flowDensity'
    finding HTML links ... done
    CellPopulation-class                    html  
    deGate                                  html  
    flowDensity-methods                     html  
    flowDensity                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/flowDensity.buildbin-libdir/00LOCK-flowDensity/00new/flowDensity/help/flowDensity.html
    getPeaks                                html  
    getflowFrame                            html  
    nmRemove                                html  
    notSubFrame                             html  
    plotDens                                html  
** building package indices
** installing vignettes
   'flowDensity.Rmd' 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'flowDensity' ...
** testing if installed package can be loaded
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
* MD5 sums
packaged installation of 'flowDensity' as flowDensity_1.28.0.zip
* DONE (flowDensity)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'flowDensity' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowDensity.Rcheck/examples_i386/flowDensity-Ex.timings

nameusersystemelapsed
CellPopulation-class000
deGate0.390.062.57
flowDensity0.090.000.09
getPeaks0.050.000.05
getflowFrame0.180.000.19
nmRemove0.440.013.39
notSubFrame0.220.025.11
plotDens0.360.020.38

flowDensity.Rcheck/examples_x64/flowDensity-Ex.timings

nameusersystemelapsed
CellPopulation-class0.020.000.02
deGate0.280.020.29
flowDensity0.060.020.08
getPeaks0.050.000.04
getflowFrame0.060.000.07
nmRemove0.290.000.29
notSubFrame 0.13 0.0123.61
plotDens0.270.000.27