Multiple platform build/check report for BioC 3.14 - CHECK results for multiSight on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: multiSight

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiSight.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings multiSight_1.2.0.tar.gz

StartedAt: 2022-04-12 23:28:18 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:35:53 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 455.3 seconds

RetCode: 0

Status: OK

CheckDir: multiSight.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiSight.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings multiSight_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/multiSight.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'multiSight/DESCRIPTION' ... OK
* this is package 'multiSight' version '1.2.0'
* package encoding: UTF-8
* 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 'multiSight' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  CeCILL + file LICENSE
* 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
mod_understand_server: no visible global function definition for
  'keytypes'
Undefined global functions or variables:
  keytypes
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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
correlationNetworkInference 5.79   0.22    6.01
buildFeatTable              0.17   0.08   29.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
correlationNetworkInference 6.17   0.06    6.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/multiSight.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/multiSight_1.2.0.tar.gz && rm -rf multiSight.buildbin-libdir && mkdir multiSight.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multiSight.buildbin-libdir multiSight_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL multiSight_1.2.0.zip && rm multiSight_1.2.0.tar.gz multiSight_1.2.0.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
 53 2027k   53 1090k    0     0  1266k      0  0:00:01 --:--:--  0:00:01 1266k
100 2027k  100 2027k    0     0  1550k      0  0:00:01  0:00:01 --:--:-- 1551k

install for i386

* installing *source* package 'multiSight' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'multiSight'
    finding HTML links ... done
    assessPerformance_Biosigner             html  
    assessPerformance_Diablo                html  
    biosignerRes                            html  
    buildFeatTable                          html  
    convertToEntrezid                       html  
    correlationNetworkInference             html  
    deseqRes                                html  
    diabloRes                               html  
    enrichResList                           html  
    enrichWP                                html  
    getDataSelectedFeatures                 html  
    mod_hypothesisGenerator_server          html  
    mod_understand_server                   html  
    mod_understand_ui                       html  
    mod_user_input_server                   html  
    mutualInformationNI                     html  
    omic2                                   html  
    partialCorrelationNI                    html  
    pubmedInsight                           html  
    runFeatureNumberTuning                  html  
    runMultiDeseqAnalysis                   html  
    runMultiEnrichment                      html  
    runMultiEnrichment_result               html  
    runSPLSDA                               html  
    runSVMRFmodels_Biosigner                html  
    run_app                                 html  
    splitDatatoTrainTest                    html  
    stoufferTable                           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 'multiSight' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multiSight' as multiSight_1.2.0.zip
* DONE (multiSight)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'multiSight' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> # library(multiSight)
> 
> # test_check("multiSight")
> 
> proc.time()
   user  system elapsed 
   0.46    0.09    0.54


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> # library(multiSight)
> 
> # test_check("multiSight")
> 
> proc.time()
   user  system elapsed 
   0.51    0.04    0.53

name	user	system	elapsed
assessPerformance_Biosigner	0.11	0.00	0.11
assessPerformance_Diablo	0.16	0.01	0.18
buildFeatTable	0.17	0.08	29.11
convertToEntrezid	0	0	0
correlationNetworkInference	5.79	0.22	6.01
getDataSelectedFeatures	0.04	0.01	0.05
mutualInformationNI	0.04	0.05	0.11
partialCorrelationNI	0.11	0.00	0.11
runMultiDeseqAnalysis	0.08	0.00	0.08
runMultiEnrichment	0.52	0.12	0.64
runSPLSDA	0.05	0.00	0.04
runSVMRFmodels_Biosigner	0.04	0.00	0.05
splitDatatoTrainTest	0.04	0.00	0.03
stoufferTable	0.73	0.02	0.75

name	user	system	elapsed
assessPerformance_Biosigner	0.11	0.00	0.11
assessPerformance_Diablo	0.17	0.00	0.17
buildFeatTable	0.13	0.08	0.29
convertToEntrezid	0	0	0
correlationNetworkInference	6.17	0.06	6.24
getDataSelectedFeatures	0.04	0.03	0.08
mutualInformationNI	0.11	0.02	0.12
partialCorrelationNI	0.11	0.01	0.13
runMultiDeseqAnalysis	0.11	0.00	0.11
runMultiEnrichment	0.47	0.05	0.51
runSPLSDA	0.02	0.03	0.05
runSVMRFmodels_Biosigner	0.03	0.00	0.03
splitDatatoTrainTest	0.00	0.01	0.02
stoufferTable	0.47	0.07	0.53

CHECK results for multiSight on tokay2

Summary

Command output

Installation output

Tests output

Example timings