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This page was generated on 2025-08-02 12:08 -0400 (Sat, 02 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 827/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.33.1  (landing page)
Sean Davis
Snapshot Date: 2025-08-01 13:25 -0400 (Fri, 01 Aug 2025)
git_url: https://git.bioconductor.org/packages/GenomicDataCommons
git_branch: devel
git_last_commit: b59db7b
git_last_commit_date: 2025-05-12 14:24:20 -0400 (Mon, 12 May 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GenomicDataCommons on lconway

To the developers/maintainers of the GenomicDataCommons package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDataCommons.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: GenomicDataCommons
Version: 1.33.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicDataCommons_1.33.1.tar.gz
StartedAt: 2025-08-01 21:05:31 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 21:07:25 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 113.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDataCommons.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicDataCommons_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GenomicDataCommons.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘GenomicDataCommons/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicDataCommons’ 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 ‘GenomicDataCommons’ 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 ... 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK


Installation output

GenomicDataCommons.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GenomicDataCommons’ ...
** this is package ‘GenomicDataCommons’ version ‘1.33.1’
** using staged installation
** R
** 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 (GenomicDataCommons)

Tests output

GenomicDataCommons.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "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(GenomicDataCommons)

Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':

    filter

> 
> test_check("GenomicDataCommons")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 46 ]
> 
> proc.time()
   user  system elapsed 
  5.252   0.413  10.395 

Example timings

GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.0970.0130.839
available_expand0.0130.0010.074
available_fields0.0310.0020.128
available_values0.0350.0020.648
constants0.0010.0010.000
count0.0570.0030.368
default_fields0.0350.0030.137
entity_name0.0390.0030.163
expand0.0730.0040.292
faceting0.0580.0050.213
field_description0.1570.0070.498
filtering0.4480.0201.695
gdc_cache0.0010.0000.001
gdc_client0.0040.0070.022
gdc_clinical0.6350.0311.373
gdc_token0.0000.0000.001
gdcdata0.2110.0110.731
grep_fields0.0270.0030.067
id_field0.0280.0010.076
ids0.1950.0091.034
manifest0.1190.0030.345
mapping0.0160.0020.049
query0.0680.0030.167
readDNAcopy0.2910.0300.327
readHTSeqFile0.0740.0060.079
response0.0450.0020.220
results0.0420.0020.212
results_all0.0480.0020.327
select0.0810.0040.366
slicing0.0000.0000.001
status0.0080.0000.057
transfer000
write_manifest0.1200.0030.396