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This page was generated on 2025-08-28 11:42 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
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: 2025-08-25 13:40 -0400 (Mon, 25 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 24.04.3 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    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: 2025-08-26 10:00:19 -0000 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 10:03:31 -0000 (Tue, 26 Aug 2025)
EllapsedTime: 192.1 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
gdc_clinical      0.710  0.035   5.110
filtering         0.573  0.025  14.812
gdcdata           0.239  0.008   5.508
ids               0.234  0.000   8.398
field_description 0.189  0.011   7.761
count             0.080  0.000   5.531
* 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 
  6.623   0.521  32.878 

Example timings

GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.0690.0241.735
available_expand0.0180.0000.240
available_fields0.0420.0000.715
available_values0.0390.0041.266
constants0.0010.0000.001
count0.0800.0005.531
default_fields0.0400.0000.703
entity_name0.0500.0000.503
expand0.1040.0001.456
faceting0.0690.0001.107
field_description0.1890.0117.761
filtering 0.573 0.02514.812
gdc_cache0.0010.0000.003
gdc_client0.0020.0030.005
gdc_clinical0.7100.0355.110
gdc_token0.0010.0000.000
gdcdata0.2390.0085.508
grep_fields0.0270.0000.456
id_field0.0330.0041.142
ids0.2340.0008.398
manifest0.1290.0041.347
mapping0.0110.0070.241
query0.1400.0041.639
readDNAcopy0.3040.0360.340
readHTSeqFile0.0770.0040.083
response0.0540.0000.996
results0.0540.0000.797
results_all0.0730.0041.301
select0.0940.0161.884
slicing0.0010.0000.000
status0.0140.0000.264
transfer000
write_manifest0.0820.0080.880