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This page was generated on 2024-07-19 17:41 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 2139/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.24.0  (landing page)
Marcel Ramos
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/TCGAutils
git_branch: RELEASE_3_19
git_last_commit: 9707923
git_last_commit_date: 2024-04-30 11:06:17 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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    NA  


CHECK results for TCGAutils on kjohnson1

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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2024-07-19 13:15:37 -0400 (Fri, 19 Jul 2024)
EndedAt: 2024-07-19 13:25:15 -0400 (Fri, 19 Jul 2024)
EllapsedTime: 578.0 seconds
RetCode: 0
Status:   OK  
CheckDir: TCGAutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TCGAutils.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.24.0’
* 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            45.816  2.189  56.450
TCGAprimaryTumors       22.888  1.611  31.268
trimColData             23.146  1.180  30.376
imputeAssay             19.804  0.908  26.013
curatedTCGAData-helpers 19.730  0.934  25.849
oncoPrintTCGA           17.107  0.830  24.832
ID-translation           2.040  0.065   9.224
* 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-3.19-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/4.4-arm64/Resources/library’
* installing *source* package ‘TCGAutils’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 
 17.672   0.702  30.278 

Example timings

TCGAutils.Rcheck/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation2.0400.0659.224
TCGAbarcode0.0010.0000.001
TCGAbiospec0.0260.0060.035
TCGAprimaryTumors22.888 1.61131.268
TCGAsampleSelect0.0100.0040.021
builds0.1250.0030.144
curatedTCGAData-helpers19.730 0.93425.849
findGRangesCols0.0030.0000.004
generateMap0.0320.0010.039
getFileName0.0300.0051.626
imputeAssay19.804 0.90826.013
makeGRangesListFromCopyNumber0.4630.0192.465
makeGRangesListFromExonFiles0.1870.0080.208
mergeColData0.3010.0180.346
oncoPrintTCGA17.107 0.83024.832
simplifyTCGA45.816 2.18956.450
trimColData23.146 1.18030.376