Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-11-26 15:05:23 -0500 (Fri, 26 Nov 2021).

CHECK results for MetaCyto on tokay2

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? here 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 1096/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.16.0  (landing page)
Zicheng Hu
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/MetaCyto
git_branch: RELEASE_3_14
git_last_commit: 7e80a3f
git_last_commit_date: 2021-10-26 12:39:42 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MetaCyto
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaCyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaCyto_1.16.0.tar.gz
StartedAt: 2021-11-26 01:06:26 -0500 (Fri, 26 Nov 2021)
EndedAt: 2021-11-26 01:20:37 -0500 (Fri, 26 Nov 2021)
EllapsedTime: 851.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaCyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaCyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaCyto_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaCyto.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaCyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaCyto' version '1.16.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
autoCluster.batch   89.44  46.23  135.77
labelCluster        84.83  33.55  118.37
searchCluster.batch 31.78  10.47   42.25
searchCluster       10.00   3.50   13.50
flowSOM.MC          11.89   0.28   12.17
densityPlot          7.45   4.14   11.60
clusterStats         7.53   3.96   11.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
autoCluster.batch   82.36  47.69  130.09
labelCluster        74.31  34.05  108.37
searchCluster.batch 23.28  11.34   34.62
flowSOM.MC          13.94   0.17   14.11
searchCluster        8.68   3.70   12.38
densityPlot          6.75   3.89   10.64
clusterStats         6.47   3.42    9.89
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaCyto.Rcheck/00check.log'
for details.



Installation output

MetaCyto.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MetaCyto_1.16.0.tar.gz && rm -rf MetaCyto.buildbin-libdir && mkdir MetaCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaCyto.buildbin-libdir MetaCyto_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MetaCyto_1.16.0.zip && rm MetaCyto_1.16.0.tar.gz MetaCyto_1.16.0.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  2255k      0 --:--:-- --:--:-- --:--:-- 2263k

install for i386

* installing *source* package 'MetaCyto' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MetaCyto'
    finding HTML links ... done
    autoCluster.batch                       html  
    clusterStats                            html  
    collectData                             html  
    densityPlot                             html  
    fcsInfoParser                           html  
    filterLabels                            html  
    findCutoff                              html  
    flowHC                                  html  
    flowSOM.MC                              html  
    glmAnalysis                             html  
    labelCluster                            html  
    labelSummary                            html  
    markerFinder                            html  
    metaAnalysis                            html  
    nameUpdator                             html  
    panelSummary                            html  
    plotGA                                  html  
    preprocessing                           html  
    preprocessing.batch                     html  
    sampleInfoParser                        html  
    searchCluster                           html  
    searchCluster.batch                     html  
    set2Frame                               html  
** 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

install for x64

* installing *source* package 'MetaCyto' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaCyto' as MetaCyto_1.16.0.zip
* DONE (MetaCyto)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MetaCyto' successfully unpacked and MD5 sums checked

Tests output


Example timings

MetaCyto.Rcheck/examples_i386/MetaCyto-Ex.timings

nameusersystemelapsed
autoCluster.batch 89.44 46.23135.77
clusterStats 7.53 3.9611.48
collectData0.020.010.03
densityPlot 7.45 4.1411.60
fcsInfoParser0.200.020.21
filterLabels000
findCutoff1.780.982.77
flowHC2.910.163.06
flowSOM.MC11.89 0.2812.17
glmAnalysis0.270.000.27
labelCluster 84.83 33.55118.37
labelSummary0.270.000.27
markerFinder0.010.000.01
metaAnalysis0.080.010.10
nameUpdator0.980.081.06
panelSummary0.020.000.01
plotGA0.660.020.68
preprocessing0.390.000.39
preprocessing.batch1.110.041.15
sampleInfoParser000
searchCluster10.0 3.513.5
searchCluster.batch31.7810.4742.25
set2Frame0.110.020.13

MetaCyto.Rcheck/examples_x64/MetaCyto-Ex.timings

nameusersystemelapsed
autoCluster.batch 82.36 47.69130.09
clusterStats6.473.429.89
collectData0.030.000.03
densityPlot 6.75 3.8910.64
fcsInfoParser0.150.030.19
filterLabels000
findCutoff1.600.952.54
flowHC2.760.052.82
flowSOM.MC13.94 0.1714.11
glmAnalysis0.360.000.36
labelCluster 74.31 34.05108.37
labelSummary0.300.000.29
markerFinder0.010.000.02
metaAnalysis0.160.000.16
nameUpdator1.610.051.65
panelSummary0.020.000.02
plotGA0.470.000.47
preprocessing0.510.020.53
preprocessing.batch1.560.031.59
sampleInfoParser000
searchCluster 8.68 3.7012.38
searchCluster.batch23.2811.3434.62
set2Frame0.120.000.13