Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-06-24 11:05:29 -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

CHECK results for MetaCyto on nebbiolo2


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 1114/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.19.0  (landing page)
Zicheng Hu
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/MetaCyto
git_branch: master
git_last_commit: 68653e0
git_last_commit_date: 2022-04-26 11:45:07 -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  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MetaCyto
Version: 1.19.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings MetaCyto_1.19.0.tar.gz
StartedAt: 2022-06-23 20:34:39 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 20:40:09 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 329.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaCyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings MetaCyto_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MetaCyto.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘1.19.0’
* 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   87.293 12.023  99.320
labelCluster        70.556  9.208  79.764
searchCluster.batch 22.682  2.944  25.627
flowSOM.MC          10.780  0.124  10.906
searchCluster        7.636  0.904   8.539
densityPlot          7.269  0.228   7.497
clusterStats         6.305  0.884   7.189
* 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-3.16-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.



Installation output

MetaCyto.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MetaCyto
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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.batch87.29312.02399.320
clusterStats6.3050.8847.189
collectData0.0260.0000.027
densityPlot7.2690.2287.497
fcsInfoParser0.0750.0000.075
filterLabels0.0010.0000.001
findCutoff1.3170.2481.565
flowHC1.9490.0682.017
flowSOM.MC10.780 0.12410.906
glmAnalysis0.2700.0000.271
labelCluster70.556 9.20879.764
labelSummary0.2560.0080.264
markerFinder0.0220.0000.023
metaAnalysis0.10.00.1
nameUpdator1.0280.0121.040
panelSummary0.0140.0000.014
plotGA0.4400.0080.448
preprocessing0.4190.0120.431
preprocessing.batch1.0510.0201.071
sampleInfoParser0.0030.0000.003
searchCluster7.6360.9048.539
searchCluster.batch22.682 2.94425.627
set2Frame0.1160.0040.121