Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-14 13:20:45 -0400 (Fri, 14 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4383
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4137
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4202
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

CHECK results for TCGAutils on nebbiolo1


To the developers/maintainers of the TCGAutils package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1989/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.16.1  (landing page)
Marcel Ramos
Snapshot Date: 2022-10-13 13:55:08 -0400 (Thu, 13 Oct 2022)
git_url: https://git.bioconductor.org/packages/TCGAutils
git_branch: RELEASE_3_15
git_last_commit: c707a87
git_last_commit_date: 2022-10-11 13:11:53 -0400 (Tue, 11 Oct 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: TCGAutils
Version: 1.16.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TCGAutils_1.16.1.tar.gz
StartedAt: 2022-10-13 21:58:09 -0400 (Thu, 13 Oct 2022)
EndedAt: 2022-10-13 22:04:28 -0400 (Thu, 13 Oct 2022)
EllapsedTime: 378.8 seconds
RetCode: 0
Status:   OK  
CheckDir: TCGAutils.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TCGAutils_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TCGAutils.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.16.1’
* 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 ‘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 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘GenomicRanges:::.normarg_field’
  ‘S4Vectors:::selectSome’
  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                       31.911  3.379  36.075
TCGAprimaryTumors                  17.413  2.237  20.621
trimColData                        15.480  1.483  17.789
makeSummarizedExperimentFromGISTIC 14.210  2.697  19.736
curatedTCGAData-helpers            12.883  1.396  15.018
imputeAssay                        12.795  1.373  15.012
oncoPrintTCGA                      11.785  1.271  14.768
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.



Installation output

TCGAutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TCGAutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> library(testthat)
> 
> library(TCGAutils)
> 
> test_check("TCGAutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
 14.024   0.959  18.328 

Example timings

TCGAutils.Rcheck/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation1.3600.1193.530
TCGAbarcode0.0010.0000.001
TCGAbiospec0.0320.0040.036
TCGAprimaryTumors17.413 2.23720.621
TCGAsampleSelect0.0080.0000.008
builds0.1220.0040.126
curatedTCGAData-helpers12.883 1.39615.018
findGRangesCols0.0030.0000.002
generateMap0.0310.0000.030
getFileName0.0170.0030.336
imputeAssay12.795 1.37315.012
makeGRangesListFromCopyNumber0.5970.0671.573
makeGRangesListFromExonFiles0.2360.0360.268
makeSummarizedExperimentFromGISTIC14.210 2.69719.736
mergeColData0.2680.0320.300
oncoPrintTCGA11.785 1.27114.768
simplifyTCGA31.911 3.37936.075
trimColData15.480 1.48317.789