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This page was generated on 2022-06-24 11:08:19 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

BUILD results for openCyto on lconway


To the developers/maintainers of the openCyto package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/openCyto.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 1361/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 2.9.0  (landing page)
Mike Jiang ,Jake Wagner
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/openCyto
git_branch: master
git_last_commit: 79c52b4
git_last_commit_date: 2022-04-26 11:16:45 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'flowStats' which is not available
lconwaymacOS 12.2.1 Monterey / x86_64  OK    ERROR  skippedskipped

Summary

Package: openCyto
Version: 2.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data openCyto
StartedAt: 2022-06-23 17:19:43 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 17:21:28 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 105.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data openCyto
###
##############################################################################
##############################################################################


* checking for file ‘openCyto/DESCRIPTION’ ... OK
* preparing ‘openCyto’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HowToAutoGating.Rmd’ using rmarkdown
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
Warning: replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats'
Loading required package: ggplot2
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
--- finished re-building ‘HowToAutoGating.Rmd’

--- re-building ‘HowToWriteCSVTemplate.Rmd’ using rmarkdown
expanding pop: +/- to cd4+/cd4-

expanding pop: +/-+/-

splitting the row that has multiple parents: 'cd4,cd8'
--- finished re-building ‘HowToWriteCSVTemplate.Rmd’

--- re-building ‘openCytoVignette.Rmd’ using knitr
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Quitting from lines 69-71 (openCytoVignette.Rmd) 
Error: processing vignette 'openCytoVignette.Rmd' failed with diagnostics:
Metric information not available for this family/device
--- failed re-building ‘openCytoVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘openCytoVignette.Rmd’

Error: Vignette re-building failed.
Execution halted