Back to Multiple platform build/check report for BioC 3.15
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-03-18 11:07:31 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 flowMerge on riesling1


To the developers/maintainers of the flowMerge package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowMerge.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 668/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMerge 2.43.0  (landing page)
Greg Finak
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/flowMerge
git_branch: master
git_last_commit: 4a18b18
git_last_commit_date: 2021-10-26 11:54:06 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowMerge
Version: 2.43.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowMerge.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings flowMerge_2.43.0.tar.gz
StartedAt: 2022-03-17 19:07:10 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:08:36 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 85.4 seconds
RetCode: 0
Status:   OK  
CheckDir: flowMerge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowMerge.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings flowMerge_2.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/flowMerge.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowMerge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowMerge' version '2.43.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC', 'multicore'

Depends: includes the non-default packages:
  'graph', 'feature', 'flowClust', 'Rgraphviz', 'foreach', 'snow'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'flowMerge' 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
* 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
Packages in Depends field not imported from:
  'foreach' 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initPFlowMerge: no visible global function definition for
  'clusterEvalQ'
mergeClusters: no visible global function definition for '%dopar%'
mergeClusters: no visible global function definition for 'foreach'
mergeClusters: no visible global function definition for '%do%'
pFlowClust : <anonymous>: no visible global function definition for
  'clusterMap'
pFlowClust: no visible global function definition for 'clusterMap'
ptree: no visible global function definition for 'subGraph'
ptree: no visible global function definition for 'nodes'
ptree : <anonymous>: no visible global function definition for
  'nodeDataDefaults<-'
ptree : <anonymous>: no visible global function definition for
  'nodeData<-'
ptree : <anonymous>: no visible global function definition for
  'subGraph'
ptree : <anonymous>: no visible global function definition for
  'nodeRenderInfo<-'
Undefined global functions or variables:
  %do% %dopar% clusterEvalQ clusterMap foreach nodeData<-
  nodeDataDefaults<- nodeRenderInfo<- nodes subGraph
* 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 ... 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/flowMerge.Rcheck/00check.log'
for details.



Installation output

flowMerge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL flowMerge
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'flowMerge' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowMerge'
    finding HTML links ... done
    NENT                                    html  
    checkForRemoteErrors                    html  
    fitPiecewiseLinreg-methods              html  
    fitPiecewiseLinreg                      html  
    flagOutliers-methods                    html  
    flagOutliers                            html  
    flowClust.res                           html  
    flowMerge-class                         html  
    finding level-2 HTML links ... done

    flowMerge-internal                      html  
    flowMerge-package                       html  
    flowObj-class                           html  
    flowObj                                 html  
    initPFlowMerge                          html  
    map                                     html  
    merge-methods                           html  
    merge                                   html  
    mergeClusters                           html  
    mergeClusters2                          html  
    pFlowClust                              html  
    pFlowMerge                              html  
    plot-methods                            html  
    ptree                                   html  
    show-methods                            html  
    split-methods                           html  
    summary-methods                         html  
    updateU                                 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
* DONE (flowMerge)
Making 'packages.html' ... done

Tests output


Example timings

flowMerge.Rcheck/flowMerge-Ex.timings

nameusersystemelapsed
NENT000
fitPiecewiseLinreg000
flowClust.res000
flowMerge-package000
flowObj000
map0.010.000.02
merge-methods000
merge000
pFlowMerge0.020.000.01
plot-methods000
updateU000