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This page was generated on 2022-10-19 13:20:30 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 MetaCyto on nebbiolo1


To the developers/maintainers of the MetaCyto package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaCyto.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1126/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.18.0  (landing page)
Zicheng Hu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MetaCyto
git_branch: RELEASE_3_15
git_last_commit: 81aa622
git_last_commit_date: 2022-04-26 11:45:07 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'FlowSOM' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MetaCyto
Version: 1.18.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MetaCyto_1.18.0.tar.gz
StartedAt: 2022-10-18 20:29:14 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:35:18 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 364.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaCyto.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MetaCyto_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MetaCyto.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaCyto’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MetaCyto’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
collectData: no visible binding for global variable ‘parameter_name’
collectData: no visible binding for global variable ‘value’
panelSummary: no visible binding for global variable ‘antibodies’
panelSummary: no visible binding for global variable ‘value’
plotGA: no visible binding for global variable ‘lower’
plotGA: no visible binding for global variable ‘upper’
searchCluster : <anonymous>: no visible binding for global variable
  ‘triS’
Undefined global functions or variables:
  antibodies lower parameter_name triS upper value
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
autoCluster.batch   88.570 12.240 100.816
labelCluster        74.558  8.545  83.108
searchCluster.batch 24.489  3.056  27.545
flowSOM.MC          10.643  0.119  10.763
searchCluster        8.835  1.408  10.243
clusterStats         6.837  1.168   8.006
densityPlot          6.725  0.596   7.320
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.



Installation output

MetaCyto.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MetaCyto
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘MetaCyto’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (MetaCyto)

Tests output


Example timings

MetaCyto.Rcheck/MetaCyto-Ex.timings

nameusersystemelapsed
autoCluster.batch 88.570 12.240100.816
clusterStats6.8371.1688.006
collectData0.0330.0000.034
densityPlot6.7250.5967.320
fcsInfoParser0.0760.0000.076
filterLabels0.0010.0000.001
findCutoff1.6650.0321.696
flowHC1.7860.0681.854
flowSOM.MC10.643 0.11910.763
glmAnalysis0.2470.0120.260
labelCluster74.558 8.54583.108
labelSummary0.2540.0040.258
markerFinder0.0270.0010.028
metaAnalysis0.1200.0070.128
nameUpdator1.1230.0331.156
panelSummary0.0160.0000.017
plotGA0.4510.0030.454
preprocessing0.4110.0000.411
preprocessing.batch1.1300.0041.134
sampleInfoParser0.0000.0030.003
searchCluster 8.835 1.40810.243
searchCluster.batch24.489 3.05627.545
set2Frame0.1250.0080.133