Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2025-08-09 12:06 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1829/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTNsurvival 1.33.1  (landing page)
Clarice Groeneveld , Mauro A. A. Castro
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/RTNsurvival
git_branch: devel
git_last_commit: 824130f
git_last_commit_date: 2025-07-23 14:55:28 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for RTNsurvival on nebbiolo2

To the developers/maintainers of the RTNsurvival package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTNsurvival.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RTNsurvival
Version: 1.33.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RTNsurvival_1.33.1.tar.gz
StartedAt: 2025-08-09 02:12:12 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 02:16:08 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 236.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RTNsurvival.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RTNsurvival_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RTNsurvival.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘RTNsurvival/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTNsurvival’ version ‘1.33.1’
* 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 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 code 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TNS-class.Rd: TNI-class
  tni2tnsPreprocess-methods.Rd: TNI-class, tni.preprocess
  tnsAREA3-methods.Rd: tni.area3
  tnsGSEA2-methods.Rd: tni.gsea2, TNI-class
  tnsPlotGSEA2-methods.Rd: tna.plot.gsea2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/RTNsurvival.Rcheck/00check.log’
for details.


Installation output

RTNsurvival.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RTNsurvival
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘RTNsurvival’ ...
** this is package ‘RTNsurvival’ version ‘1.33.1’
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RTNsurvival)

Tests output

RTNsurvival.Rcheck/tests/runTests.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 -- Sat Aug  9 02:15:48 2025 
*********************************************** 
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 
 10.869   0.516  11.373 

Example timings

RTNsurvival.Rcheck/RTNsurvival-Ex.timings

nameusersystemelapsed
TNS.data0.0000.0000.002
hclust_semisupervised0.0530.0040.055
tni2tnsPreprocess-methods0.3440.0060.351
tnsAREA3-methods1.1790.0541.235
tnsCox-methods1.4250.0711.497
tnsCoxInteraction-methods1.3560.0131.369
tnsGSEA2-methods0.7930.0040.798
tnsGet-methods0.8440.0250.867
tnsInteraction-methods1.3060.0161.323
tnsKM-methods0.8360.0070.844
tnsKmInteraction-methods1.3490.0121.360
tnsPlotCovariates-methods2.0230.1312.155
tnsPlotCox-methods1.4700.0661.536
tnsPlotCoxInteraction-methods0.7890.0020.792
tnsPlotGSEA2-methods1.9480.0652.013
tnsPlotKM-methods1.5660.0061.572
tnsPlotKmInteraction-methods0.8150.0100.825
tnsPlotSRE-methods0.8930.0160.910
tnsSRD-methods1.4540.0111.465
tnsSRE-methods0.8650.0060.871
tnsStratification0.0000.0010.000