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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 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" 4536
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 796/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 3.5.4  (landing page)
Ogan Mancarci
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/gemma.R
git_branch: devel
git_last_commit: 73d1354
git_last_commit_date: 2025-06-23 21:53:56 -0400 (Mon, 23 Jun 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    ERROR  


CHECK results for gemma.R on taishan

To the developers/maintainers of the gemma.R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemma.R.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: gemma.R
Version: 3.5.4
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gemma.R_3.5.4.tar.gz
StartedAt: 2025-08-01 06:49:15 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 07:06:12 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 1016.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: gemma.R.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gemma.R_3.5.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gemma.R.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.5.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘gemma.R’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                              user system elapsed
get_dataset_object                           9.276  0.242  12.348
get_gene_differential_expression_values      2.245  0.099   7.580
dot-get_gene_differential_expression_values  1.643  0.028   7.329
get_dataset_processed_expression             1.171  0.039   7.559
update_result                                0.705  0.012   5.432
get_dataset_differential_expression_analyses 0.547  0.023   7.075
get_datasets                                 0.221  0.012   5.493
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─gemma.R::get_platform_datasets(1, offset = 0) at testPlatformEndpoints.R:30:5
    2. │ ├─gemma.R:::.body(...)
    3. │ │ └─base::eval(requestExpr, envir = envWhere)
    4. │ │   └─base::eval(requestExpr, envir = envWhere)
    5. │ └─httr::GET(...)
    6. │   └─httr:::request_perform(req, hu$handle$handle)
    7. │     ├─httr:::request_fetch(req$output, req$url, handle)
    8. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
    9. │       └─curl::curl_fetch_memory(url, handle = handle)
   10. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 181 ]
  Error: Test failures
  Execution halted
* 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 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/gemma.R.Rcheck/00check.log’
for details.


Installation output

gemma.R.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL gemma.R
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘gemma.R’ ...
** this is package ‘gemma.R’ version ‘3.5.4’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (gemma.R)

Tests output

gemma.R.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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(dplyr)

Attaching package: 'dplyr'

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

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> # Prevent certificate issues for GitHub actions
> options(gemma.SSL = FALSE)
> # get gemma api path if it's set in the environment
> gemma.R:::setGemmaPath('prod')
[1] "https://gemma.msl.ubc.ca/rest/v2/"
> print(gemma.R:::gemmaPath())
[1] "https://gemma.msl.ubc.ca/rest/v2/"
> test_check("gemma.R")
Loading required package: gemma.R
[ FAIL 2 | WARN 0 | SKIP 4 | PASS 181 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Bioconductor (4): 'testCaches.R:37:3', 'testConvenience.R:15:5',
  'testConvenience.R:37:5', 'testDatasetEndpoints.R:88:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testOrderSanity.R:95:9'): Multiple sanity checks for expression/differential expression values and sample metadata ──
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [gemma.msl.ubc.ca]:
Connection timed out after 10001 milliseconds
Backtrace:
     ▆
  1. ├─gemma.R::get_differential_expression_values(dt) at testOrderSanity.R:95:9
  2. │ └─base::lapply(...)
  3. │   └─gemma.R (local) FUN(X[[i]], ...)
  4. │     └─gemma.R:::.getResultSets(x, memoised = memoised)
  5. │       ├─gemma.R:::.body(...)
  6. │       │ └─base::eval(requestExpr, envir = envWhere)
  7. │       │   └─base::eval(requestExpr, envir = envWhere)
  8. │       └─httr::GET(...)
  9. │         └─httr:::request_perform(req, hu$handle$handle)
 10. │           ├─httr:::request_fetch(req$output, req$url, handle)
 11. │           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 12. │             └─curl::curl_fetch_memory(url, handle = handle)
 13. └─curl:::raise_libcurl_error(...)
── Error ('testPlatformEndpoints.R:30:5'): getPlatformDatasets queries work ────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [gemma.msl.ubc.ca]:
Connection timed out after 10002 milliseconds
Backtrace:
     ▆
  1. ├─gemma.R::get_platform_datasets(1, offset = 0) at testPlatformEndpoints.R:30:5
  2. │ ├─gemma.R:::.body(...)
  3. │ │ └─base::eval(requestExpr, envir = envWhere)
  4. │ │   └─base::eval(requestExpr, envir = envWhere)
  5. │ └─httr::GET(...)
  6. │   └─httr:::request_perform(req, hu$handle$handle)
  7. │     ├─httr:::request_fetch(req$output, req$url, handle)
  8. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
  9. │       └─curl::curl_fetch_memory(url, handle = handle)
 10. └─curl:::raise_libcurl_error(...)

[ FAIL 2 | WARN 0 | SKIP 4 | PASS 181 ]
Error: Test failures
Execution halted

Example timings

gemma.R.Rcheck/gemma.R-Ex.timings

nameusersystemelapsed
dot-getResultSets0.0000.0000.001
dot-get_dataset_expression_for_genes1.2040.0884.165
dot-get_gene_differential_expression_values1.6430.0287.329
filter_properties0.0380.0000.041
forget_gemma_memoised0.0160.0120.075
gemma_call0.0130.0040.229
get_annotation_children0.0080.0030.212
get_annotation_parents0.0130.0000.213
get_child_terms0.0210.0000.236
get_dataset_annotations0.010.000.22
get_dataset_differential_expression_analyses0.5470.0237.075
get_dataset_expression0.8750.0254.963
get_dataset_expression_for_genes0.3170.0201.306
get_dataset_object 9.276 0.24212.348
get_dataset_platforms0.0160.0000.638
get_dataset_processed_expression1.1710.0397.559
get_dataset_quantitation_types0.0140.0000.228
get_dataset_raw_expression1.0180.0284.165
get_dataset_samples0.2550.0161.024
get_datasets0.2210.0125.493
get_datasets_by_ids0.0530.0000.481
get_differential_expression_values0.2800.0084.885
get_gene_differential_expression_values2.2450.0997.580
get_gene_go_terms0.0480.0000.881
get_gene_locations0.0270.0000.499
get_gene_probes0.0250.0040.326
get_genes0.0260.0040.467
get_platform_annotations0.5320.0162.605
get_platform_datasets0.0430.0000.496
get_platform_element_genes0.0180.0080.256
get_platforms_by_ids0.0350.0000.485
get_result_sets0.0520.0040.490
get_taxa0.0130.0000.219
get_taxa_by_ids0.0120.0000.218
get_taxon_datasets0.0340.0150.289
make_design0.8320.0361.436
search_annotations0.0090.0040.220
search_datasets0.0430.0000.579
search_gemma0.1040.0000.736
update_result0.7050.0125.432