Multiple platform build/check report for BioC 3.14 - CHECK results for PathoStat 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: PathoStat

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathoStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PathoStat_1.20.0.tar.gz

StartedAt: 2022-04-13 00:17:38 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:25:03 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 444.5 seconds

RetCode: 0

Status: OK

CheckDir: PathoStat.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathoStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PathoStat_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PathoStat.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 'PathoStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PathoStat' version '1.20.0'
* 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 'PathoStat' 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 ... NOTE
Namespaces in Imports field not imported from:
  'ComplexHeatmap' 'RColorBrewer'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
Bootstrap_LOOCV_LR_AUC         14.75   0.55   15.30
getSignatureFromMultipleGlmnet  9.02   0.02    9.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
Bootstrap_LOOCV_LR_AUC         16.65   0.09   16.75
getSignatureFromMultipleGlmnet 11.12   0.00   11.13
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/PathoStat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PathoStat_1.20.0.tar.gz && rm -rf PathoStat.buildbin-libdir && mkdir PathoStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PathoStat.buildbin-libdir PathoStat_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PathoStat_1.20.0.zip && rm PathoStat_1.20.0.tar.gz PathoStat_1.20.0.zip
###
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  % 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  951k  100  951k    0     0   932k      0  0:00:01  0:00:01 --:--:--  933k
100  951k  100  951k    0     0   932k      0  0:00:01  0:00:01 --:--:--  932k

install for i386

* installing *source* package 'PathoStat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PathoStat'
    finding HTML links ... done
    Bootstrap_LOOCV_LR_AUC                  html  
    Chisq_Test_Pam                          html  
    Fisher_Test_Pam                         html  
    GET_PAM                                 html  
    LOOAUC_simple_multiple_noplot_one_df    html  
    LOOAUC_simple_multiple_one_df           html  
    PathoStat-class                         html  
    TranslateIdToTaxLevel                   html  
    Wilcox_Test_df                          html  
    findRAfromCount                         html  
    findTaxonMat                            html  
    findTaxonomy                            html  
    findTaxonomy300                         html  
    formatTaxTable                          html  
    getShinyInput                           html  
    getShinyInputCombat                     html  
    getShinyInputOrig                       html  
    getSignatureFromMultipleGlmnet          html  
    grepTid                                 html  
    loadPathoscopeReports                   html  
    loadPstat                               html  
    log2CPM                                 html  
    percent                                 html  
    phyloseq_to_edgeR                       html  
    plotPCAPlotly                           html  
    plotPCoAPlotly                          html  
    pstat_data                              html  
    readPathoscopeData                      html  
    runPathoStat                            html  
    savePstat                               html  
    setShinyInput                           html  
    setShinyInputCombat                     html  
    setShinyInputOrig                       html  
    summarizeTable                          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 'PathoStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PathoStat' as PathoStat_1.20.0.zip
* DONE (PathoStat)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PathoStat' 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(PathoStat)
> 
> test_check("PathoStat")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  13.67    1.09   14.75


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(PathoStat)
> 
> test_check("PathoStat")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  10.84    0.48   11.32

name	user	system	elapsed
Bootstrap_LOOCV_LR_AUC	14.75	0.55	15.30
Chisq_Test_Pam	0	0	0
Fisher_Test_Pam	0.02	0.00	0.02
GET_PAM	0	0	0
LOOAUC_simple_multiple_noplot_one_df	3.25	0.00	3.25
LOOAUC_simple_multiple_one_df	3.11	0.05	3.16
PathoStat-class	0.04	0.00	0.05
TranslateIdToTaxLevel	0	0	0
Wilcox_Test_df	0.02	0.00	0.01
findRAfromCount	0.14	0.00	0.14
findTaxonMat	0.08	0.00	0.11
findTaxonomy	0.06	0.01	0.08
findTaxonomy300	0.06	0.00	0.06
getShinyInput	0	0	0
getShinyInputCombat	0	0	0
getShinyInputOrig	0	0	0
getSignatureFromMultipleGlmnet	9.02	0.02	9.04
grepTid	0	0	0
loadPathoscopeReports	0	0	0
loadPstat	0	0	0
log2CPM	0	0	0
percent	0	0	0
phyloseq_to_edgeR	0.06	0.00	0.06
plotPCAPlotly	0.30	0.08	0.37
plotPCoAPlotly	0.20	0.01	0.24
readPathoscopeData	0.08	0.00	0.08
runPathoStat	0.12	0.00	0.12
savePstat	0.02	0.00	0.02
setShinyInput	0	0	0
setShinyInputCombat	0	0	0
setShinyInputOrig	0	0	0
summarizeTable	0	0	0

name	user	system	elapsed
Bootstrap_LOOCV_LR_AUC	16.65	0.09	16.75
Chisq_Test_Pam	0.02	0.00	0.01
Fisher_Test_Pam	0.02	0.00	0.02
GET_PAM	0	0	0
LOOAUC_simple_multiple_noplot_one_df	3.28	0.02	3.30
LOOAUC_simple_multiple_one_df	3.31	0.00	3.31
PathoStat-class	0.06	0.00	0.06
TranslateIdToTaxLevel	0	0	0
Wilcox_Test_df	0.02	0.00	0.02
findRAfromCount	0.15	0.00	0.15
findTaxonMat	0.08	0.02	0.10
findTaxonomy	0.08	0.00	0.07
findTaxonomy300	0.08	0.00	0.08
getShinyInput	0	0	0
getShinyInputCombat	0	0	0
getShinyInputOrig	0	0	0
getSignatureFromMultipleGlmnet	11.12	0.00	11.13
grepTid	0	0	0
loadPathoscopeReports	0	0	0
loadPstat	0	0	0
log2CPM	0	0	0
percent	0	0	0
phyloseq_to_edgeR	0.05	0.01	0.06
plotPCAPlotly	0.17	0.08	0.25
plotPCoAPlotly	0.11	0.05	0.16
readPathoscopeData	0.05	0.00	0.04
runPathoStat	0.08	0.00	0.08
savePstat	0	0	0
setShinyInput	0	0	0
setShinyInputCombat	0	0	0
setShinyInputOrig	0	0	0
summarizeTable	0.01	0.00	0.02

CHECK results for PathoStat on tokay2

Summary

Command output

Installation output

Tests output

Example timings