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This page was generated on 2022-06-24 11:06:44 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaCyto.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MetaCyto_1.19.0.tar.gz
StartedAt: 2022-06-24 03:11:20 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 03:17:29 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 368.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaCyto.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaCyto.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MetaCyto_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MetaCyto.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 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   88.95  16.12  105.17
labelCluster        75.68  10.82   86.61
searchCluster.batch 23.01   3.73   26.83
flowSOM.MC          13.07   1.75   14.87
searchCluster        7.72   1.19    8.92
clusterStats         7.08   1.06    8.14
densityPlot          6.73   1.25    8.00
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/MetaCyto.Rcheck/00check.log'
for details.



Installation output

MetaCyto.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/MetaCyto_1.19.0.tar.gz && rm -rf MetaCyto.buildbin-libdir && mkdir MetaCyto.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaCyto.buildbin-libdir MetaCyto_1.19.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL MetaCyto_1.19.0.zip && rm MetaCyto_1.19.0.tar.gz MetaCyto_1.19.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  914k  100  914k    0     0  4581k      0 --:--:-- --:--:-- --:--:-- 4619k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'MetaCyto' as MetaCyto_1.19.0.zip
* DONE (MetaCyto)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'MetaCyto' successfully unpacked and MD5 sums checked

Tests output


Example timings

MetaCyto.Rcheck/MetaCyto-Ex.timings

nameusersystemelapsed
autoCluster.batch 88.95 16.12105.17
clusterStats7.081.068.14
collectData0.030.000.03
densityPlot6.731.258.00
fcsInfoParser0.220.000.22
filterLabels000
findCutoff1.780.322.10
flowHC2.350.062.42
flowSOM.MC13.07 1.7514.87
glmAnalysis0.290.010.30
labelCluster75.6810.8286.61
labelSummary0.240.000.23
markerFinder0.010.000.02
metaAnalysis0.080.020.09
nameUpdator1.080.011.11
panelSummary0.030.000.03
plotGA0.470.000.47
preprocessing0.390.020.42
preprocessing.batch1.300.061.38
sampleInfoParser000
searchCluster7.721.198.92
searchCluster.batch23.01 3.7326.83
set2Frame0.110.000.14