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This page was generated on 2025-01-16 12:08 -0500 (Thu, 16 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4489
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4387
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

Package 1205/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.28.0  (landing page)
Zicheng Hu
Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 2025)
git_url: https://git.bioconductor.org/packages/MetaCyto
git_branch: RELEASE_3_20
git_last_commit: 9c13bf5
git_last_commit_date: 2024-10-29 10:23:48 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for MetaCyto on merida1

To the developers/maintainers of the MetaCyto package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MetaCyto
Version: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2025-01-14 05:42:02 -0500 (Tue, 14 Jan 2025)
EndedAt: 2025-01-14 05:51:00 -0500 (Tue, 14 Jan 2025)
EllapsedTime: 538.0 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_1.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MetaCyto.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaCyto’ version ‘1.28.0’
* 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 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 code 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   105.336 14.636 123.287
labelCluster         88.458 11.387 106.523
searchCluster.batch  26.352  3.316  32.807
flowSOM.MC           22.149  2.447  28.831
searchCluster         8.927  1.131  10.752
densityPlot           8.585  1.119  10.776
clusterStats          8.501  1.128  10.147
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.


Installation output

MetaCyto.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MetaCyto
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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.batch105.336 14.636123.287
clusterStats 8.501 1.12810.147
collectData0.0580.0070.077
densityPlot 8.585 1.11910.776
fcsInfoParser0.1950.0100.226
filterLabels0.0030.0000.004
findCutoff1.9020.2542.338
flowHC3.3490.0703.607
flowSOM.MC22.149 2.44728.831
glmAnalysis0.6360.0190.665
labelCluster 88.458 11.387106.523
labelSummary0.9330.0111.077
markerFinder0.0470.0030.059
metaAnalysis0.2160.0120.261
nameUpdator2.6350.0583.087
panelSummary0.0300.0040.038
plotGA1.3160.0231.544
preprocessing1.0670.0231.236
preprocessing.batch2.6940.0913.270
sampleInfoParser0.0070.0020.011
searchCluster 8.927 1.13110.752
searchCluster.batch26.352 3.31632.807
set2Frame0.2530.0130.272