##############################################################################
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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_3.7.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/gemma.R.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.7.1’
* 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 ... ERROR
Running examples in ‘gemma.R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .get_dataset_expression_for_genes
> ### Title: Retrieve the expression data matrix of a set of datasets and
> ###   genes
> ### Aliases: .get_dataset_expression_for_genes
> ### Keywords: internal
> 
> ### ** Examples
> 
> get_dataset_expression_for_genes("GSE2018", genes = c(10225, 2841))
Error in .body(fname = fname, validators = validators, endpoint = endpoint,  : 
  https://gemma.msl.ubc.ca/rest/v2/datasets/GSE2018?&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Calls: get_dataset_expression_for_genes -> get_datasets_by_ids -> .body
Execution halted
* 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_platforms_by_ids(1, file = file) at testProcessors.R:3:5
   2.   └─gemma.R:::.body(...)
  ── Error ('testTaxonEndpoints.R:2:5'): getTaxonInfo queries work ───────────────
  Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/taxa/mouse%2Chuman
  503: Service Unavailable. Gemma might be under maintenance.
  Backtrace:
      ▆
   1. └─gemma.R:::get_taxa_by_ids(c("mouse", "human")) at testTaxonEndpoints.R:2:5
   2.   └─gemma.R:::.body(...)
  
  [ FAIL 33 | WARN 1 | SKIP 5 | PASS 23 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/gemma.R.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gemma.R
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘gemma.R’ ...
** this is package ‘gemma.R’ version ‘3.7.1’
** 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)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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 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
Saving _problems/testCaches-9.R
Saving _problems/testCaches-107.R
Saving _problems/testCaches-140.R
Saving _problems/testCompression-6.R
Saving _problems/testConvenience-48.R
Saving _problems/testConvenience-54.R
Saving _problems/testConvenience-68.R
Saving _problems/testConvenience-95.R
Saving _problems/testConvenience-123.R
Saving _problems/testConvenience-129.R
Saving _problems/testConvenience-136.R
Saving _problems/testDatasetEndpoints-2.R
Saving _problems/testDatasetEndpoints-24.R
Saving _problems/testDatasetEndpoints-35.R
Saving _problems/testDatasetEndpoints-48.R
Saving _problems/testDatasetEndpoints-61.R
Saving _problems/testDatasetEndpoints-74.R
Saving _problems/testEmpty-3.R
Saving _problems/testEmpty-14.R
Saving _problems/testEmpty-25.R
Saving _problems/testGeneEndpoints-2.R
Saving _problems/testGeneEndpoints-13.R
Saving _problems/testGeneEndpoints-24.R
Saving _problems/testGeneEndpoints-36.R
Saving _problems/testMisc-2.R
Saving _problems/testMisc-11.R
Saving _problems/testOrderSanity-2.R
Saving _problems/testOrderSanity-29.R
Saving _problems/testPlatformEndpoints-2.R
Saving _problems/testPlatformEndpoints-17.R
Saving _problems/testPlatformEndpoints-59.R
Saving _problems/testProcessors-3.R
Saving _problems/testTaxonEndpoints-2.R
[ FAIL 33 | WARN 1 | SKIP 5 | PASS 23 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On Bioconductor (4): 'testCaches.R:37:3', 'testConvenience.R:15:5',
  'testConvenience.R:37:5', 'testDatasetEndpoints.R:88:5'
• empty test (1): 'testConvenience.R:1:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testCaches.R:5:3'): caches work for base functions ──────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/search?query=bipolar&taxon=human&limit=100&resultTypes=ubic.gemma.model.expression.experiment.ExpressionExperiment
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. ├─... %>% summary at testCaches.R:5:3
 2. ├─base::summary(.)
 3. ├─microbenchmark::microbenchmark(...)
 4. └─gemma.R::search_gemma(...)
 5.   └─gemma.R:::.body(...)
── Error ('testCaches.R:105:3'): custom cache paths work ───────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/GSE2018/samples?useProcessedQuantitationType=true
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. ├─... %>% summary at testCaches.R:105:3
 2. ├─base::summary(.)
 3. ├─microbenchmark::microbenchmark(...)
 4. ├─gemma.R::get_dataset_object(test_gse, memoised = FALSE)
 5. │ └─unique_sets %>% ...
 6. └─base::lapply(...)
 7.   └─gemma.R (local) FUN(X[[i]], ...)
 8.     └─gemma.R::get_dataset_samples(dataset, memoised = memoised)
 9.       └─gemma.R:::.body(...)
── Error ('testCaches.R:136:5'): in memory caches work ─────────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/search?query=bipolar&taxon=human&limit=100&resultTypes=ubic.gemma.model.expression.experiment.ExpressionExperiment
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. ├─... %>% summary at testCaches.R:136:5
 2. ├─base::summary(.)
 3. ├─microbenchmark::microbenchmark(...)
 4. └─gemma.R::search_gemma(...)
 5.   └─gemma.R:::.body(...)
── Error ('testCompression.R:6:5'): Compressed inputs work ─────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/resultSets?filter=baselineGroup.characteristics.value%20%3D%20disease&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_result_sets(filter = "baselineGroup.characteristics.value = disease") at testCompression.R:6:5
 2.   └─gemma.R:::.body(...)
── Error ('testConvenience.R:48:5'): get_dataset_object with multiple datasets and genes ──
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/549/samples?useProcessedQuantitationType=true
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. ├─gemma.R::get_dataset_object(datasets, genes, type = "tidy") at testConvenience.R:48:5
 2. │ └─unique_sets %>% ...
 3. └─base::lapply(...)
 4.   └─gemma.R (local) FUN(X[[i]], ...)
 5.     └─gemma.R::get_dataset_samples(dataset, memoised = memoised)
 6.       └─gemma.R:::.body(...)
── Error ('testConvenience.R:54:5'): get_dataset_object with aggeration methods ──
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/549/samples?useProcessedQuantitationType=true
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. ├─gemma.R::get_dataset_object(549, consolidate = "average") at testConvenience.R:54:5
 2. │ └─unique_sets %>% ...
 3. └─base::lapply(...)
 4.   └─gemma.R (local) FUN(X[[i]], ...)
 5.     └─gemma.R::get_dataset_samples(dataset, memoised = memoised)
 6.       └─gemma.R:::.body(...)
── Error ('testConvenience.R:68:5'): get_dataset_object with resultSets ────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/442/analyses/differential
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_differential_expression_analyses(442) at testConvenience.R:68:5
 2.   └─gemma.R:::.body(...)
── Error ('testConvenience.R:95:5'): getDatasetDE works properly ───────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/2/analyses/differential
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_differential_expression_values(2) at testConvenience.R:95:5
 2.   └─gemma.R::get_dataset_differential_expression_analyses(dataset)
 3.     └─gemma.R:::.body(...)
── Error ('testConvenience.R:123:5'): getGenomeVersions works properly ─────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/taxa/9606%2C10090%2C10116%2C4932%2C7955%2C7227%2C6239
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_taxa() at testConvenience.R:123:5
 2.   └─gemma.R:::get_taxa_by_ids(...)
 3.     └─gemma.R:::.body(...)
── Error ('testConvenience.R:129:5'): gemmaCall works properly ─────────────────
Error in `gemma_call("datasets/{dataset}/svd", dataset = 1)`: datasets/{dataset}/svd
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::gemma_call("datasets/{dataset}/svd", dataset = 1) at testConvenience.R:129:5
── Error ('testConvenience.R:134:5'): get_all_pages works properly ─────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1%2C2%2C3?&offset=0&limit=1&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. ├─... %>% get_all_pages(step_size = 1) at testConvenience.R:134:5
 2. ├─gemma.R::get_all_pages(., step_size = 1)
 3. └─gemma.R::get_datasets_by_ids(datasets = c(1, 2, 3), limit = 1)
 4.   └─gemma.R:::.body(...)
── Error ('testDatasetEndpoints.R:2:5'): getDatasetsInfo queries work ──────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1?&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_datasets_by_ids(1) at testDatasetEndpoints.R:2:5
 2.   └─gemma.R:::.body(...)
── Error ('testDatasetEndpoints.R:24:5'): datasetPlatforms queries work ────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1/platforms
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_platforms(1) at testDatasetEndpoints.R:24:5
 2.   └─gemma.R:::.body(...)
── Error ('testDatasetEndpoints.R:35:5'): datasetSamples queries work ──────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1/samples?useProcessedQuantitationType=true
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_samples(1) at testDatasetEndpoints.R:35:5
 2.   └─gemma.R:::.body(...)
── Error ('testDatasetEndpoints.R:48:5'): datasetDEA queries work ──────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/2/analyses/differential
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_differential_expression_analyses(2) at testDatasetEndpoints.R:48:5
 2.   └─gemma.R:::.body(...)
── Error ('testDatasetEndpoints.R:61:5'): datasetAnnotations queries work ──────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1/annotations
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_annotations(1) at testDatasetEndpoints.R:61:5
 2.   └─gemma.R:::.body(...)
── Error ('testDatasetEndpoints.R:74:5'): get_dataset_expression_for_genes work ──
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1%2C4?&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_expression_for_genes(...) at testDatasetEndpoints.R:74:5
 2.   └─gemma.R::get_datasets_by_ids(datasets = datasets)
 3.     └─gemma.R:::.body(...)
── Error ('testEmpty.R:3:5'): Empty output on simple processors ────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1?&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_datasets_by_ids(1) at testEmpty.R:3:5
 2.   └─gemma.R:::.body(...)
── Error ('testEmpty.R:14:5'): Empty output on DEAs ────────────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/1/analyses/differential
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_differential_expression_analyses(1) at testEmpty.R:14:5
 2.   └─gemma.R:::.body(...)
── Error ('testEmpty.R:25:5'): Empty output on resultsets ──────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/resultSets?datasets=1&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_result_sets(1) at testEmpty.R:25:5
 2.   └─gemma.R:::.body(...)
── Error ('testGeneEndpoints.R:2:5'): getGenesInfo queries work ────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/genes/1859/
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_genes(1859) at testGeneEndpoints.R:2:5
 2.   └─gemma.R:::.body(...)
── Error ('testGeneEndpoints.R:13:5'): getGeneLocation queries work ────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/genes/1859/locations
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_gene_locations(1859) at testGeneEndpoints.R:13:5
 2.   └─gemma.R:::.body(...)
── Error ('testGeneEndpoints.R:24:5'): getGeneProbes queries work ──────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/genes/1859/probes?offset=0&limit=20
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_gene_probes(1859) at testGeneEndpoints.R:24:5
 2.   └─gemma.R:::.body(...)
── Error ('testGeneEndpoints.R:36:5'): searchAnnotations work ──────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/annotations/search?query=traumatic
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::search_annotations("traumatic") at testGeneEndpoints.R:36:5
 2.   └─gemma.R:::.body(...)
── Error ('testMisc.R:2:5'): search_gemma work ─────────────────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/search?query=bipolar&limit=100&resultTypes=ubic.gemma.model.expression.experiment.ExpressionExperiment
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::search_gemma("bipolar") at testMisc.R:2:5
 2.   └─gemma.R:::.body(...)
── Error ('testMisc.R:11:5'): test query formation ─────────────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/resultSets?datasets=1&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_result_sets(1) at testMisc.R:11:5
 2.   └─gemma.R:::.body(...)
── Error ('testOrderSanity.R:2:5'): sample ordering in outputs ─────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/2/samples?useProcessedQuantitationType=true
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_samples(2) at testOrderSanity.R:2:5
 2.   └─gemma.R:::.body(...)
── Error ('testOrderSanity.R:29:9'): Multiple sanity checks for expression/differential expression values and sample metadata ──
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/35175/samples?useProcessedQuantitationType=true
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_dataset_samples(dt) at testOrderSanity.R:29:9
 2.   └─gemma.R:::.body(...)
── Error ('testPlatformEndpoints.R:2:5'): getPlatformsInfo queries work ────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/platforms/1?&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_platforms_by_ids(1) at testPlatformEndpoints.R:2:5
 2.   └─gemma.R:::.body(...)
── Error ('testPlatformEndpoints.R:17:5'): getPlatformDatasets queries work ────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/platforms/1/datasets?offset=0&limit=20
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_platform_datasets(1) at testPlatformEndpoints.R:17:5
 2.   └─gemma.R:::.body(...)
── Error ('testPlatformEndpoints.R:59:5'): getPlatformElementsGenes queries work ──
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/platforms/GPL1355/elements/AFFX_Rat_beta-actin_M_at/genes?offset=0&limit=20
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_platform_element_genes("GPL1355", probe = "AFFX_Rat_beta-actin_M_at") at testPlatformEndpoints.R:59:5
 2.   └─gemma.R:::.body(...)
── Error ('testProcessors.R:3:5'): processor file writing ──────────────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/platforms/1?&offset=0&limit=20&sort=%2Bid
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R::get_platforms_by_ids(1, file = file) at testProcessors.R:3:5
 2.   └─gemma.R:::.body(...)
── Error ('testTaxonEndpoints.R:2:5'): getTaxonInfo queries work ───────────────
Error in `.body(fname = fname, validators = validators, endpoint = endpoint, envWhere = environment(), isFile = isFile, header = header, raw = raw, overwrite = overwrite, file = file, attributes = TRUE, in_data = in_data, open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/taxa/mouse%2Chuman
503: Service Unavailable. Gemma might be under maintenance.
Backtrace:
    ▆
 1. └─gemma.R:::get_taxa_by_ids(c("mouse", "human")) at testTaxonEndpoints.R:2:5
 2.   └─gemma.R:::.body(...)

[ FAIL 33 | WARN 1 | SKIP 5 | PASS 23 ]
Error:
! Test failures.
Execution halted