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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1802/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTNsurvival 1.31.0  (landing page)
Clarice Groeneveld , Mauro A. A. Castro
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/RTNsurvival
git_branch: devel
git_last_commit: d6d7932
git_last_commit_date: 2024-10-29 10:20:04 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for RTNsurvival on nebbiolo1

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: 1.31.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RTNsurvival_1.31.0.tar.gz
StartedAt: 2024-12-24 01:43:53 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 01:47:49 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 235.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RTNsurvival.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RTNsurvival_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RTNsurvival.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RTNsurvival/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTNsurvival’ version ‘1.31.0’
* 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 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 ... NOTE
checkRd: (-1) TNS.data.Rd:14: Lost braces
    14 |   \code{survival.data}{ A data.frame with a subset of samples in the Fletcher2013b package.}
       |                       ^
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RTNsurvival.Rcheck/00check.log’
for details.


Installation output

RTNsurvival.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL RTNsurvival
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* 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
** 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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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 -- Tue Dec 24 01:47:29 2024 
*********************************************** 
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 
 10.539   0.582  11.119 

Example timings

RTNsurvival.Rcheck/RTNsurvival-Ex.timings

nameusersystemelapsed
TNS.data0.0010.0000.002
hclust_semisupervised0.0600.0030.064
tni2tnsPreprocess-methods0.3410.0110.352
tnsAREA3-methods1.2440.0721.317
tnsCox-methods1.4780.0331.512
tnsCoxInteraction-methods0.9240.0180.943
tnsGSEA2-methods1.5300.0761.607
tnsGet-methods1.4390.0401.481
tnsInteraction-methods0.8720.0090.882
tnsKM-methods0.8860.0300.916
tnsKmInteraction-methods2.1360.0072.143
tnsPlotCovariates-methods2.0870.1372.224
tnsPlotCox-methods0.9240.0450.969
tnsPlotCoxInteraction-methods1.4850.0161.502
tnsPlotGSEA2-methods1.4860.0181.505
tnsPlotKM-methods1.7270.0151.744
tnsPlotKmInteraction-methods0.9250.0120.938
tnsPlotSRE-methods1.7710.0131.783
tnsSRD-methods0.8740.0210.896
tnsSRE-methods2.2810.0722.352
tnsStratification000