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This page was generated on 2025-08-06 13:56 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 796/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 3.5.4  (landing page)
Ogan Mancarci
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 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    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for gemma.R on kjohnson3

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.

raw results


Summary

Package: gemma.R
Version: 3.5.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemma.R_3.5.4.tar.gz
StartedAt: 2025-08-05 19:29:17 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-05 19:34:42 -0400 (Tue, 05 Aug 2025)
EllapsedTime: 324.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: gemma.R.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemma.R_3.5.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/gemma.R.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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 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                          2.849  0.115   5.303
get_gene_differential_expression_values     0.332  0.014   5.503
dot-get_gene_differential_expression_values 0.330  0.004   5.550
get_datasets                                0.056  0.008   8.044
* 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:
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On Bioconductor (4): 'testCaches.R:37:3', 'testConvenience.R:15:5',
    'testConvenience.R:37:5', 'testDatasetEndpoints.R:88:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('testCompression.R:21:5'): Compressed inputs work ──────────────────
  all(uncompressed$value.URI %in% compressed$value.URI) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 1 | SKIP 4 | PASS 197 ]
  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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/gemma.R.Rcheck/00check.log’
for details.


Installation output

gemma.R.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(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 1 | WARN 1 | SKIP 4 | PASS 197 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testCompression.R:21:5'): Compressed inputs work ──────────────────
all(uncompressed$value.URI %in% compressed$value.URI) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 1 | SKIP 4 | PASS 197 ]
Error: Test failures
Execution halted

Example timings

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

nameusersystemelapsed
dot-getResultSets000
dot-get_dataset_expression_for_genes0.3160.0212.090
dot-get_gene_differential_expression_values0.3300.0045.550
filter_properties0.0100.0010.011
forget_gemma_memoised0.0060.0200.049
gemma_call0.0020.0020.092
get_annotation_children0.0040.0010.177
get_annotation_parents0.0030.0000.088
get_child_terms0.0060.0000.105
get_dataset_annotations0.0030.0000.088
get_dataset_differential_expression_analyses0.1930.0134.663
get_dataset_expression0.3500.0232.285
get_dataset_expression_for_genes0.0640.0050.620
get_dataset_object2.8490.1155.303
get_dataset_platforms0.0040.0000.090
get_dataset_processed_expression0.4650.0272.607
get_dataset_quantitation_types0.0030.0010.095
get_dataset_raw_expression0.6380.0242.050
get_dataset_samples0.0500.0030.380
get_datasets0.0560.0088.044
get_datasets_by_ids0.0140.0020.267
get_differential_expression_values0.0980.0102.789
get_gene_differential_expression_values0.3320.0145.503
get_gene_go_terms0.0120.0000.241
get_gene_locations0.0080.0000.212
get_gene_probes0.0090.0020.260
get_genes0.0090.0010.207
get_platform_annotations0.3000.0232.519
get_platform_datasets0.0120.0020.441
get_platform_element_genes0.0040.0000.157
get_platforms_by_ids0.0090.0020.258
get_result_sets0.0140.0010.198
get_taxa0.0030.0000.090
get_taxa_by_ids0.0030.0010.089
get_taxon_datasets0.0140.0020.336
make_design0.1860.0070.525
search_annotations0.0040.0000.086
search_datasets0.0130.0010.540
search_gemma0.0350.0060.387
update_result0.1800.0133.417