Multiple platform build/check report for BioC 3.9 - CHECK report for RTNsurvival on tokay2

Package: RTNsurvival

Version: 1.8.3

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNsurvival.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTNsurvival_1.8.3.tar.gz

StartedAt: 2019-10-16 06:49:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:54:41 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 307.3 seconds

RetCode: 0

Status: OK

CheckDir: RTNsurvival.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNsurvival.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTNsurvival_1.8.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTNsurvival.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.8.3'
* 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 or elapsed time > 5s
                     user system elapsed
tnsPlotGSEA2-methods 6.39   0.58    6.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
tnsPlotGSEA2-methods 5.32   0.29    5.61
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RTNsurvival_1.8.3.tar.gz && rm -rf RTNsurvival.buildbin-libdir && mkdir RTNsurvival.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTNsurvival.buildbin-libdir RTNsurvival_1.8.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RTNsurvival_1.8.3.zip && rm RTNsurvival_1.8.3.tar.gz RTNsurvival_1.8.3.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  323k  100  323k    0     0   640k      0 --:--:-- --:--:-- --:--:--  650k

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_1.8.3.zip
* DONE (RTNsurvival)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RTNsurvival' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 -- Wed Oct 16 06:54:08 2019 
*********************************************** 
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 
   8.09    0.67    8.75


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 -- Wed Oct 16 06:54:18 2019 
*********************************************** 
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 
   9.06    0.39    9.42

name	user	system	elapsed
TNS.data	0	0	0
tni2tnsPreprocess-methods	0.43	0.03	0.45
tnsAREA3-methods	1.14	0.05	1.19
tnsCox-methods	1.48	0.10	1.58
tnsCoxInteraction-methods	1.31	0.01	1.32
tnsGSEA2-methods	2.00	0.08	2.08
tnsGet-methods	1.07	0.05	1.11
tnsInteraction-methods	1.03	0.02	1.04
tnsKM-methods	1.42	0.03	1.46
tnsKmInteraction-methods	2.12	0.06	2.18
tnsPlotCovariates-methods	3.16	0.00	3.16
tnsPlotCox-methods	1.13	0.05	1.17
tnsPlotCoxInteraction-methods	1.39	0.01	1.41
tnsPlotGSEA2-methods	6.39	0.58	6.97
tnsPlotKM-methods	1.37	0.25	1.62
tnsPlotKmInteraction-methods	1.03	0.05	1.08
tnsPlotSRE-methods	1.22	0.03	1.19
tnsSRD-methods	1.20	0.02	1.22
tnsSRE-methods	1.10	0.06	1.11
tnsStratification	0	0	0

name	user	system	elapsed
TNS.data	0	0	0
tni2tnsPreprocess-methods	0.52	0.03	0.55
tnsAREA3-methods	1.47	0.07	1.54
tnsCox-methods	1.51	0.00	1.51
tnsCoxInteraction-methods	1.55	0.04	1.61
tnsGSEA2-methods	1.50	0.07	1.56
tnsGet-methods	0.86	0.00	0.86
tnsInteraction-methods	0.89	0.00	0.89
tnsKM-methods	0.90	0.03	0.94
tnsKmInteraction-methods	0.85	0.01	0.86
tnsPlotCovariates-methods	4.06	0.10	4.16
tnsPlotCox-methods	0.86	0.03	0.89
tnsPlotCoxInteraction-methods	0.84	0.00	0.84
tnsPlotGSEA2-methods	5.32	0.29	5.61
tnsPlotKM-methods	1.68	0.02	1.70
tnsPlotKmInteraction-methods	1.13	0.03	1.16
tnsPlotSRE-methods	1.44	0.03	1.47
tnsSRD-methods	1.12	0.10	1.20
tnsSRE-methods	0.88	0.04	0.92
tnsStratification	0	0	0

CHECK report for RTNsurvival on tokay2

Summary

Command output

Installation output

Tests output

Example timings