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This page was generated on 2021-11-30 13:55:32 -0500 (Tue, 30 Nov 2021).

CHECK results for MetaCyto on merida1

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? 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 1088/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.17.0  (landing page)
Zicheng Hu
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/MetaCyto
git_branch: master
git_last_commit: a3a9965
git_last_commit_date: 2021-10-26 12:39:42 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MetaCyto
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaCyto_1.17.0.tar.gz
StartedAt: 2021-11-30 05:02:30 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 05:10:47 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 496.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaCyto.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaCyto_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MetaCyto.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.17.0’
* 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   103.838 12.864 117.298
labelCluster         90.481  8.524  99.164
searchCluster.batch  26.857  2.417  29.324
flowSOM.MC           19.195  1.938  21.193
searchCluster         8.798  0.972   9.782
clusterStats          8.380  1.007   9.425
densityPlot           7.798  0.925   8.736
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.



Installation output

MetaCyto.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MetaCyto
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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.batch103.838 12.864117.298
clusterStats8.3801.0079.425
collectData0.0540.0050.059
densityPlot7.7980.9258.736
fcsInfoParser0.1430.0030.148
filterLabels0.0030.0000.003
findCutoff1.9480.2322.184
flowHC2.9740.0413.019
flowSOM.MC19.195 1.93821.193
glmAnalysis0.5500.0110.563
labelCluster90.481 8.52499.164
labelSummary0.6950.0120.707
markerFinder0.0390.0020.040
metaAnalysis0.1800.0080.190
nameUpdator2.1110.0232.138
panelSummary0.0240.0080.034
plotGA0.8270.0090.838
preprocessing0.8590.0140.875
preprocessing.batch2.0820.0222.107
sampleInfoParser0.0050.0000.006
searchCluster8.7980.9729.782
searchCluster.batch26.857 2.41729.324
set2Frame0.1980.0040.203