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This page was generated on 2025-09-25 11:40 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 2168/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.28.0  (landing page)
Marcel Ramos
Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/TCGAutils
git_branch: RELEASE_3_21
git_last_commit: 3240a5b
git_last_commit_date: 2025-04-15 11:33:22 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for TCGAutils on merida1

To the developers/maintainers of the TCGAutils package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAutils.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: TCGAutils
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAutils_1.28.0.tar.gz
StartedAt: 2025-09-23 11:41:15 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 12:11:06 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 1790.8 seconds
RetCode: 0
Status:   OK  
CheckDir: TCGAutils.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAutils_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TCGAutils.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.28.0’
* 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 ‘TCGAutils’ 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘GenomicRanges:::.normarg_field’
  See the note in ?`:::` about the use of this operator.
* 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 (user + system) or elapsed time > 5s
                          user system  elapsed
simplifyTCGA            54.237  2.487   59.922
TCGAprimaryTumors       28.984  2.981 1075.223
trimColData             24.483  1.635   27.437
oncoPrintTCGA           23.884  1.208   45.157
imputeAssay             23.926  1.157   26.693
curatedTCGAData-helpers 22.985  1.337   25.979
ID-translation           2.335  0.066   12.061
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.


Installation output

TCGAutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TCGAutils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘TCGAutils’ ...
** this is package ‘TCGAutils’ version ‘1.28.0’
** using staged installation
** R
** data
** 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 (TCGAutils)

Tests output

TCGAutils.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(testthat)
> 
> library(TCGAutils)
> 
> test_check("TCGAutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
 27.716   1.534  35.216 

Example timings

TCGAutils.Rcheck/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation 2.335 0.06612.061
TCGAbarcode0.0010.0010.002
TCGAbiospec0.0350.0070.720
TCGAprimaryTumors 28.984 2.9811075.223
TCGAsampleSelect0.0150.0040.057
builds0.2800.0030.290
curatedTCGAData-helpers22.985 1.33725.979
findGRangesCols0.0230.0090.032
generateMap0.0660.0020.069
getFileName0.0430.0050.593
imputeAssay23.926 1.15726.693
makeGRangesListFromCopyNumber0.7030.0173.002
makeGRangesListFromExonFiles0.3330.0170.549
mergeColData0.4400.0250.470
oncoPrintTCGA23.884 1.20845.157
simplifyTCGA54.237 2.48759.922
trimColData24.483 1.63527.437