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CHECK report for RTNsurvival on tokay1

This page was generated on 2021-05-06 12:33:23 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RTNsurvival package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1595/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTNsurvival 1.14.1  (landing page)
Clarice Groeneveld , Mauro A. A. Castro
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RTNsurvival
Branch: RELEASE_3_12
Last Commit: ec16902
Last Changed Date: 2020-11-10 14:17:02 -0400 (Tue, 10 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RTNsurvival
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNsurvival.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RTNsurvival_1.14.1.tar.gz
StartedAt: 2021-05-06 06:30:11 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:35:47 -0400 (Thu, 06 May 2021)
EllapsedTime: 335.8 seconds
RetCode: 0
Status:   OK   
CheckDir: RTNsurvival.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNsurvival.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RTNsurvival_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RTNsurvival.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTNsurvival/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTNsurvival' version '1.14.1'
* 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 'RTNsurvival' 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 ... 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
tnsPlotGSEA2-methods 5.15   0.22    5.36
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: OK


Installation output

RTNsurvival.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RTNsurvival_1.14.1.tar.gz && rm -rf RTNsurvival.buildbin-libdir && mkdir RTNsurvival.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTNsurvival.buildbin-libdir RTNsurvival_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RTNsurvival_1.14.1.zip && rm RTNsurvival_1.14.1.tar.gz RTNsurvival_1.14.1.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  276k  100  276k    0     0  10.6M      0 --:--:-- --:--:-- --:--:-- 11.2M

install for i386

* installing *source* package 'RTNsurvival' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTNsurvival'
    finding HTML links ... done
    RTNsurvival-package                     html  
    TNS-class                               html  
    finding level-2 HTML links ... done

    TNS.data                                html  
    hclust_semisupervised                   html  
    tni2tnsPreprocess-methods               html  
    tnsAREA3-methods                        html  
    tnsCox-methods                          html  
    tnsCoxInteraction-methods               html  
    tnsGSEA2-methods                        html  
    tnsGet-methods                          html  
    tnsInteraction-methods                  html  
    tnsKM-methods                           html  
    tnsKmInteraction-methods                html  
    tnsPlotCovariates-methods               html  
    tnsPlotCox-methods                      html  
    tnsPlotCoxInteraction-methods           html  
    tnsPlotGSEA2-methods                    html  
    tnsPlotKM-methods                       html  
    tnsPlotKmInteraction-methods            html  
    tnsPlotSRE-methods                      html  
    tnsSRD-methods                          html  
    tnsSRE-methods                          html  
    tnsStratification                       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 'RTNsurvival' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTNsurvival' as RTNsurvival_1.14.1.zip
* DONE (RTNsurvival)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RTNsurvival' successfully unpacked and MD5 sums checked

Tests output

RTNsurvival.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> BiocGenerics:::testPackage("RTNsurvival")


RUNIT TEST PROTOCOL -- Thu May 06 06:35:28 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RTNsurvival RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  11.12    0.85   11.96 

RTNsurvival.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> BiocGenerics:::testPackage("RTNsurvival")


RUNIT TEST PROTOCOL -- Thu May 06 06:35:41 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RTNsurvival RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  11.21    0.51   11.73 

Example timings

RTNsurvival.Rcheck/examples_i386/RTNsurvival-Ex.timings

nameusersystemelapsed
TNS.data0.000.020.02
hclust_semisupervised0.060.000.06
tni2tnsPreprocess-methods0.550.030.58
tnsAREA3-methods1.330.061.39
tnsCox-methods1.640.111.75
tnsCoxInteraction-methods1.690.111.79
tnsGSEA2-methods1.670.061.74
tnsGet-methods1.550.031.58
tnsInteraction-methods1.110.041.16
tnsKM-methods1.710.071.78
tnsKmInteraction-methods1.130.001.12
tnsPlotCovariates-methods4.090.234.33
tnsPlotCox-methods1.470.201.67
tnsPlotCoxInteraction-methods1.450.101.55
tnsPlotGSEA2-methods5.150.225.36
tnsPlotKM-methods1.210.031.25
tnsPlotKmInteraction-methods1.460.041.50
tnsPlotSRE-methods2.110.472.58
tnsSRD-methods1.430.071.50
tnsSRE-methods1.740.111.84
tnsStratification000

RTNsurvival.Rcheck/examples_x64/RTNsurvival-Ex.timings

nameusersystemelapsed
TNS.data000
hclust_semisupervised0.060.000.06
tni2tnsPreprocess-methods0.340.010.36
tnsAREA3-methods1.910.051.95
tnsCox-methods1.810.101.91
tnsCoxInteraction-methods1.560.001.56
tnsGSEA2-methods0.970.000.97
tnsGet-methods2.140.002.14
tnsInteraction-methods1.470.011.48
tnsKM-methods1.390.031.43
tnsKmInteraction-methods1.700.031.73
tnsPlotCovariates-methods3.240.073.30
tnsPlotCox-methods1.700.011.72
tnsPlotCoxInteraction-methods1.090.021.11
tnsPlotGSEA2-methods4.690.154.86
tnsPlotKM-methods1.080.051.13
tnsPlotKmInteraction-methods1.090.061.15
tnsPlotSRE-methods1.080.021.10
tnsSRD-methods1.670.011.68
tnsSRE-methods1.280.021.30
tnsStratification000