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This page was generated on 2025-08-11 11:47 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 835/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.32.1  (landing page)
Sean Davis
Snapshot Date: 2025-08-07 13:40 -0400 (Thu, 07 Aug 2025)
git_url: https://git.bioconductor.org/packages/GenomicDataCommons
git_branch: RELEASE_3_21
git_last_commit: 64b24d0
git_last_commit_date: 2025-05-12 14:25:18 -0400 (Mon, 12 May 2025)
nebbiolo1Linux (Ubuntu 24.04.2 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
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    OK  


CHECK results for GenomicDataCommons on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GenomicDataCommons
Version: 1.32.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicDataCommons_1.32.1.tar.gz
StartedAt: 2025-08-08 09:36:01 -0000 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 09:38:55 -0000 (Fri, 08 Aug 2025)
EllapsedTime: 174.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDataCommons.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicDataCommons_1.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicDataCommons.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicDataCommons’ version ‘1.32.1’
* 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 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
filtering    0.568  0.099   8.304
aggregations 0.088  0.008   5.327
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GenomicDataCommons
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘GenomicDataCommons’ ...
** this is package ‘GenomicDataCommons’ version ‘1.32.1’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> 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 
  6.227   0.497  26.977 

Example timings

GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.0880.0085.327
available_expand0.0220.0120.494
available_fields0.0460.0081.181
available_values0.0470.0081.278
constants0.0010.0000.001
count0.0750.0202.333
default_fields0.0450.0040.739
entity_name0.0620.0000.982
expand0.1090.0041.543
faceting0.0740.0010.828
field_description0.2050.0031.670
filtering0.5680.0998.304
gdc_cache0.0020.0000.002
gdc_client0.0030.0020.005
gdc_clinical0.7180.1742.981
gdc_token0.0000.0000.001
gdcdata0.2480.0094.647
grep_fields0.0280.0000.266
id_field0.0390.0040.751
ids0.2390.0243.621
manifest0.1290.0120.974
mapping0.0190.0000.250
query0.1310.0120.633
readDNAcopy0.3030.0370.343
readHTSeqFile0.0770.0010.079
response0.0530.0000.620
results0.0510.0120.669
results_all0.0770.0003.920
select0.1050.0071.983
slicing000
status0.0070.0080.255
transfer000
write_manifest0.0890.0040.893