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This page was generated on 2021-10-20 12:05:19 -0400 (Wed, 20 Oct 2021).

CHECK results for PathoStat on riesling1

To the developers/maintainers of the PathoStat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PathoStat.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 1371/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PathoStat 1.19.0  (landing page)
Solaiappan Manimaran
Snapshot Date: 2021-10-19 14:50:04 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/PathoStat
git_branch: master
git_last_commit: 4c7d572
git_last_commit_date: 2021-05-19 12:23:43 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: PathoStat
Version: 1.19.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathoStat.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PathoStat_1.19.0.tar.gz
StartedAt: 2021-10-20 02:55:43 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 03:01:35 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 352.0 seconds
RetCode: 0
Status:   OK  
CheckDir: PathoStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathoStat.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PathoStat_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/PathoStat.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.19.0'
* 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         10.97   0.06   11.03
getSignatureFromMultipleGlmnet  5.94   0.00    5.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
Bootstrap_LOOCV_LR_AUC         10.55    0.1   10.64
getSignatureFromMultipleGlmnet  6.09    0.0    6.10
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/PathoStat.Rcheck/00check.log'
for details.



Installation output

PathoStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PathoStat_1.19.0.tar.gz && rm -rf PathoStat.buildbin-libdir && mkdir PathoStat.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PathoStat.buildbin-libdir PathoStat_1.19.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PathoStat_1.19.0.zip && rm PathoStat_1.19.0.tar.gz PathoStat_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  951k  100  951k    0     0  1957k      0 --:--:-- --:--:-- --:--:-- 1961k

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_1.19.0.zip
* DONE (PathoStat)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'PathoStat' successfully unpacked and MD5 sums checked

Tests output

PathoStat.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
   6.46    0.54    7.00 

PathoStat.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
   7.31    0.46    7.73 

Example timings

PathoStat.Rcheck/examples_i386/PathoStat-Ex.timings

nameusersystemelapsed
Bootstrap_LOOCV_LR_AUC10.97 0.0611.03
Chisq_Test_Pam0.020.000.01
Fisher_Test_Pam000
GET_PAM000
LOOAUC_simple_multiple_noplot_one_df2.140.002.14
LOOAUC_simple_multiple_one_df2.140.002.14
PathoStat-class0.030.000.04
TranslateIdToTaxLevel000
Wilcox_Test_df000
findRAfromCount0.110.000.10
findTaxonMat0.040.000.05
findTaxonomy0.050.000.05
findTaxonomy3000.050.000.05
getShinyInput000
getShinyInputCombat000
getShinyInputOrig000
getSignatureFromMultipleGlmnet5.940.005.94
grepTid000
loadPathoscopeReports000
loadPstat000
log2CPM000
percent000
phyloseq_to_edgeR0.050.000.05
plotPCAPlotly0.120.030.15
plotPCoAPlotly0.100.030.13
readPathoscopeData0.030.000.03
runPathoStat0.040.000.04
savePstat000
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
summarizeTable000

PathoStat.Rcheck/examples_x64/PathoStat-Ex.timings

nameusersystemelapsed
Bootstrap_LOOCV_LR_AUC10.55 0.1010.64
Chisq_Test_Pam000
Fisher_Test_Pam0.020.000.02
GET_PAM000
LOOAUC_simple_multiple_noplot_one_df2.670.002.67
LOOAUC_simple_multiple_one_df2.140.032.17
PathoStat-class0.030.000.03
TranslateIdToTaxLevel000
Wilcox_Test_df0.020.000.02
findRAfromCount0.090.000.09
findTaxonMat0.050.000.05
findTaxonomy0.030.020.05
findTaxonomy3000.030.010.04
getShinyInput000
getShinyInputCombat000
getShinyInputOrig000
getSignatureFromMultipleGlmnet6.090.006.10
grepTid000
loadPathoscopeReports000
loadPstat000
log2CPM000
percent000
phyloseq_to_edgeR0.050.000.04
plotPCAPlotly0.120.030.16
plotPCoAPlotly0.080.030.11
readPathoscopeData0.030.000.03
runPathoStat0.070.000.06
savePstat000
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
summarizeTable000