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This page was generated on 2025-09-25 11:39 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 802/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 3.4.6  (landing page)
Ogan Mancarci
Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/gemma.R
git_branch: RELEASE_3_21
git_last_commit: f0b83cd
git_last_commit_date: 2025-09-02 18:53:55 -0400 (Tue, 02 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for gemma.R on merida1

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: 3.4.6
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_3.4.6.tar.gz
StartedAt: 2025-09-23 03:54:17 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 04:04:07 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 589.8 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_3.4.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gemma.R.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.4.6’
* 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                           15.027  0.628  18.032
get_gene_differential_expression_values       3.283  0.201   7.673
dot-get_gene_differential_expression_values   2.644  0.022   9.676
get_dataset_differential_expression_analyses  0.804  0.102   5.161
* 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:
  x[2]: "GSE430"
  y[2]: "GSE5967"
  
  x[3]: "GSE685"
  y[3]: "GSE2018"
  
  x[4]: "GSE593"
  y[4]: "GSE9116"
  
  x[5]: "GSE590"
  y[5]: "GSE1922"
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 196 ]
  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-3.21-bioc/meat/gemma.R.Rcheck/00check.log’
for details.


Installation output

gemma.R.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘gemma.R’ ...
** this is package ‘gemma.R’ version ‘3.4.6’
** 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 RC (2025-06-05 r88288) -- "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(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 196 ]

══ 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 
── Failure ('testPlatformEndpoints.R:21:5'): getPlatformDatasets queries work ──
dat[, c(experiment.shortName, experiment.name, experiment.sampleCount)] not equal to c(...).
59/60 mismatches
x[1]: "GSE2018"
y[1]: "GSE15653"

x[2]: "GSE430"
y[2]: "GSE5967"

x[3]: "GSE685"
y[3]: "GSE2018"

x[4]: "GSE593"
y[4]: "GSE9116"

x[5]: "GSE590"
y[5]: "GSE1922"

[ FAIL 2 | WARN 0 | SKIP 4 | PASS 196 ]
Error: Test failures
Execution halted

Example timings

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

nameusersystemelapsed
dot-getResultSets0.0000.0010.001
dot-get_dataset_expression_for_genes2.0710.1293.267
dot-get_gene_differential_expression_values2.6440.0229.676
filter_properties0.0720.0090.121
forget_gemma_memoised0.0300.0980.175
gemma_call0.0150.0220.114
get_annotation_children0.0170.0020.084
get_annotation_parents0.0210.0030.088
get_child_terms0.0350.0020.128
get_dataset_annotations0.0170.0020.094
get_dataset_differential_expression_analyses0.8040.1025.161
get_dataset_expression1.2620.2133.285
get_dataset_expression_for_genes0.5210.0171.010
get_dataset_object15.027 0.62818.032
get_dataset_platforms0.0280.0030.238
get_dataset_processed_expression1.5580.1833.839
get_dataset_quantitation_types0.0180.0040.305
get_dataset_raw_expression1.3050.1362.923
get_dataset_samples0.4420.0480.808
get_datasets0.3740.0593.940
get_datasets_by_ids0.0860.0060.247
get_differential_expression_values0.3700.0743.702
get_gene_differential_expression_values3.2830.2017.673
get_gene_go_terms0.0760.0030.344
get_gene_locations0.0400.0030.233
get_gene_probes0.0490.0080.295
get_genes0.0470.0040.221
get_platform_annotations0.7270.0802.091
get_platform_datasets0.0680.0060.430
get_platform_element_genes0.0230.0010.120
get_platforms_by_ids0.0520.0030.234
get_result_sets0.0790.0030.250
get_taxa0.0190.0020.087
get_taxa_by_ids0.0170.0010.087
get_taxon_datasets0.0800.0120.355
make_design1.3630.0541.780
search_annotations0.0220.0040.095
search_datasets0.0750.0110.436
search_gemma0.2060.0530.680
update_result1.0310.0323.553