Package: RTNsurvival

Version: 1.4.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTNsurvival_1.4.5.tar.gz

StartedAt: 2018-10-16 23:50:53 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:53:18 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 145.0 seconds

RetCode: 0

Status:  OK

CheckDir: RTNsurvival.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTNsurvival_1.4.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RTNsurvival.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTNsurvival/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTNsurvival’ version ‘1.4.5’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
tnsPlotGSEA2-methods 4.902  0.376   5.319
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RTNsurvival
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RTNsurvival’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTNsurvival)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Tue Oct 16 23:53:12 2018 
*********************************************** 
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 
  5.879   0.438   6.321 

name	user	system	elapsed
TNS.data	0.018	0.004	0.020
tni2tnsPreprocess-methods	0.369	0.017	0.387
tnsAREA3-methods	0.937	0.049	0.989
tnsCox-methods	1.481	0.163	1.648
tnsCoxInteraction-methods	2.416	0.180	2.608
tnsGSEA2-methods	1.431	0.110	1.546
tnsGet-methods	1.187	0.090	1.285
tnsInteraction-methods	2.286	0.147	2.452
tnsKM-methods	1.236	0.121	1.364
tnsKmInteraction-methods	2.345	0.153	2.510
tnsPlotCox-methods	1.149	0.113	1.269
tnsPlotCoxInteraction-methods	1.978	0.182	2.165
tnsPlotGSEA2-methods	4.902	0.376	5.319
tnsPlotKM-methods	1.474	0.148	1.637
tnsPlotKmInteraction-methods	1.831	0.253	2.093
tnsStratification	0.001	0.000	0.002