Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MetaCyto on malbec1

This page was generated on 2019-04-16 11:53:09 -0400 (Tue, 16 Apr 2019).

Package 919/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.4.1
Zicheng Hu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MetaCyto
Branch: RELEASE_3_8
Last Commit: cb601de
Last Changed Date: 2019-01-04 13:38:04 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MetaCyto
Version: 1.4.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MetaCyto_1.4.1.tar.gz
StartedAt: 2019-04-16 01:16:04 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:20:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 276.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MetaCyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MetaCyto_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MetaCyto.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.1’
* 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 or elapsed time > 5s
                      user system elapsed
autoCluster.batch   64.468  9.304  74.039
labelCluster        54.160  3.268  57.559
searchCluster.batch 17.744  2.688  20.509
flowSOM.MC          15.096  0.036  15.163
searchCluster        5.816  0.964   6.810
densityPlot          5.292  0.896   6.210
clusterStats         5.044  0.652   5.719
* 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-3.8-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.



Installation output

MetaCyto.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MetaCyto
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘MetaCyto’ ...
** 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
* DONE (MetaCyto)

Tests output


Example timings

MetaCyto.Rcheck/MetaCyto-Ex.timings

nameusersystemelapsed
autoCluster.batch64.468 9.30474.039
clusterStats5.0440.6525.719
collectData0.0520.0080.065
densityPlot5.2920.8966.210
fcsInfoParser0.1160.0000.137
filterLabels0.0040.0000.001
findCutoff0.9440.0000.946
flowHC2.2760.0202.297
flowSOM.MC15.096 0.03615.163
glmAnalysis0.4760.0000.478
labelCluster54.160 3.26857.559
labelSummary0.6160.0000.620
markerFinder0.0360.0000.034
metaAnalysis0.1320.0000.132
nameUpdator1.6240.0001.624
panelSummary0.0240.0040.065
plotGA0.7120.0040.718
preprocessing0.6760.0000.677
preprocessing.batch1.6080.0001.610
sampleInfoParser0.0040.0000.005
searchCluster5.8160.9646.810
searchCluster.batch17.744 2.68820.509
set2Frame0.1160.0000.115