Last updated on 2025-07-24 06:49:31 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.4 | 2.23 | 34.49 | 36.72 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.4 | 1.53 | 26.36 | 27.89 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.4 | 87.01 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.4 | 98.08 | OK | |||
| r-devel-windows-x86_64 | 1.0.4 | 4.00 | 63.00 | 67.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.4 | 2.55 | 33.07 | 35.62 | ERROR | |
| r-release-linux-x86_64 | 1.0.4 | 2.25 | 82.68 | 84.93 | OK | |
| r-release-macos-arm64 | 1.0.4 | 67.00 | OK | |||
| r-release-macos-x86_64 | 1.0.4 | 176.00 | OK | |||
| r-release-windows-x86_64 | 1.0.4 | 4.00 | 66.00 | 70.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.4 | 53.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.4 | 93.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.4 | 5.00 | 72.00 | 77.00 | ERROR |
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> if (!requireNamespace('vcr')) {
+ "Skipping tests as the vcr webmockr package is integral to testing yet unavailable."
+ } else {
+ test_check("magmaR")
+ }
Loading required namespace: vcr
Loading required package: magmaR
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-matrix.R:10:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-matrix.R:8:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "rna_seq") at test-matrix.R:10:5
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-meta.R:10:9'): retrieveMetadata, same branch ───────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-meta.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "biospecimen") at test-meta.R:10:9
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:11:9'): query_list ─────────────────────────────────────
Error in `.perform_curl_get(fxn = "/query", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::query(...) at test-query.R:11:9
4. └─magmaR:::.query(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:29:9'): query_df ───────────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:27:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-query.R:29:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:10:9'): retrieve & retrieveJSON work with minimal input ──
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(targ, "example", "subject") at test-retrieve.R:10:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:35:9'): retrieve works with targetted input, 1att ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:34:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:35:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:50:9'): retrieve works with targetted input, 1rec ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:49:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:50:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:65:9'): retrieveJSON can hide templates ─────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:64:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(...) at test-retrieve.R:65:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:10:7'): retrieveTemplate ─────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:9:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveTemplate(targ, "example") at test-special.R:10:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:17:7'): retrieveModels ───────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:16:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveModels(targ, "example") at test-special.R:17:7
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:24:7'): retrieveIds ──────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:23:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-special.R:24:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:31:7'): retrieveAttributes ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:30:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "subject") at test-special.R:31:7
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:38:9'): retrieveParentName ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:37:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveParentName(targ, "example", "demographic") at test-special.R:38:9
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-update.R:12:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-update.R:11:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") at test-update.R:12:5
4. └─magmaR::retrieveIds(target, projectName, modelName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 1.0.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Download.Rmd’ using rmarkdown
Quitting from Download.Rmd:235-256 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.perform_curl_get()`:
! You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
---
Backtrace:
▆
1. └─magmaR::retrieveProjects(target = prod)
2. └─magmaR:::.perform_curl_get(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Download.Rmd' failed with diagnostics:
You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
--- failed re-building ‘Download.Rmd’
--- re-building ‘Upload.Rmd’ using rmarkdown
Quitting from Upload.Rmd:136-151 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.perform_curl_get()`:
! You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
---
Backtrace:
▆
1. └─magmaR::updateValues(...)
2. └─magmaR::retrieveTemplate(target, projectName)
3. └─magmaR:::.retrieve(...)
4. └─magmaR:::.perform_curl_get(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
--- failed re-building ‘Upload.Rmd’
SUMMARY: processing the following files failed:
‘Download.Rmd’ ‘Upload.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> if (!requireNamespace('vcr')) {
+ "Skipping tests as the vcr webmockr package is integral to testing yet unavailable."
+ } else {
+ test_check("magmaR")
+ }
Loading required namespace: vcr
Loading required package: magmaR
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-matrix.R:10:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-matrix.R:8:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "rna_seq") at test-matrix.R:10:5
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-meta.R:10:9'): retrieveMetadata, same branch ───────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-meta.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "biospecimen") at test-meta.R:10:9
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:11:9'): query_list ─────────────────────────────────────
Error in `.perform_curl_get(fxn = "/query", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::query(...) at test-query.R:11:9
4. └─magmaR:::.query(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:29:9'): query_df ───────────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:27:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-query.R:29:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:10:9'): retrieve & retrieveJSON work with minimal input ──
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(targ, "example", "subject") at test-retrieve.R:10:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:35:9'): retrieve works with targetted input, 1att ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:34:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:35:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:50:9'): retrieve works with targetted input, 1rec ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:49:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:50:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:65:9'): retrieveJSON can hide templates ─────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:64:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(...) at test-retrieve.R:65:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:10:7'): retrieveTemplate ─────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:9:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveTemplate(targ, "example") at test-special.R:10:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:17:7'): retrieveModels ───────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:16:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveModels(targ, "example") at test-special.R:17:7
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:24:7'): retrieveIds ──────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:23:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-special.R:24:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:31:7'): retrieveAttributes ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:30:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "subject") at test-special.R:31:7
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:38:9'): retrieveParentName ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:37:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveParentName(targ, "example", "demographic") at test-special.R:38:9
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-update.R:12:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-update.R:11:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") at test-update.R:12:5
4. └─magmaR::retrieveIds(target, projectName, modelName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.4
Check: tests
Result: ERROR
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library("testthat")
> if (!requireNamespace('vcr')) {
+ "Skipping tests as the vcr webmockr package is integral to testing yet unavailable."
+ } else {
+ test_check("magmaR")
+ }
Loading required namespace: vcr
Loading required package: magmaR
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-matrix.R:10:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-matrix.R:8:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "rna_seq") at test-matrix.R:10:5
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-meta.R:10:9'): retrieveMetadata, same branch ───────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-meta.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "biospecimen") at test-meta.R:10:9
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:11:9'): query_list ─────────────────────────────────────
Error in `.perform_curl_get(fxn = "/query", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::query(...) at test-query.R:11:9
4. └─magmaR:::.query(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:29:9'): query_df ───────────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:27:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-query.R:29:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:10:9'): retrieve & retrieveJSON work with minimal input ──
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(targ, "example", "subject") at test-retrieve.R:10:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:35:9'): retrieve works with targetted input, 1att ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:34:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:35:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:50:9'): retrieve works with targetted input, 1rec ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:49:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:50:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:65:9'): retrieveJSON can hide templates ─────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:64:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(...) at test-retrieve.R:65:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:10:7'): retrieveTemplate ─────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:9:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveTemplate(targ, "example") at test-special.R:10:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:17:7'): retrieveModels ───────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:16:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveModels(targ, "example") at test-special.R:17:7
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:24:7'): retrieveIds ──────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:23:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-special.R:24:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:31:7'): retrieveAttributes ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:30:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "subject") at test-special.R:31:7
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:38:9'): retrieveParentName ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:37:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveParentName(targ, "example", "demographic") at test-special.R:38:9
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-update.R:12:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-update.R:11:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") at test-update.R:12:5
4. └─magmaR::retrieveIds(target, projectName, modelName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.0.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'Download.Rmd' using rmarkdown
Quitting from Download.Rmd:235-256 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.perform_curl_get()`:
! You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
---
Backtrace:
▆
1. └─magmaR::retrieveProjects(target = prod)
2. └─magmaR:::.perform_curl_get(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Download.Rmd' failed with diagnostics:
You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
--- failed re-building 'Download.Rmd'
--- re-building 'Upload.Rmd' using rmarkdown
Quitting from Upload.Rmd:136-151 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.perform_curl_get()`:
! You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
---
Backtrace:
▆
1. └─magmaR::updateValues(...)
2. └─magmaR::retrieveTemplate(target, projectName)
3. └─magmaR:::.retrieve(...)
4. └─magmaR:::.perform_curl_get(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
--- failed re-building 'Upload.Rmd'
SUMMARY: processing the following files failed:
'Download.Rmd' 'Upload.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.4
Check: tests
Result: ERROR
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library("testthat")
> if (!requireNamespace('vcr')) {
+ "Skipping tests as the vcr webmockr package is integral to testing yet unavailable."
+ } else {
+ test_check("magmaR")
+ }
Loading required namespace: vcr
Loading required package: magmaR
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-matrix.R:10:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-matrix.R:8:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "rna_seq") at test-matrix.R:10:5
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-meta.R:10:9'): retrieveMetadata, same branch ───────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-meta.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "biospecimen") at test-meta.R:10:9
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:11:9'): query_list ─────────────────────────────────────
Error in `.perform_curl_get(fxn = "/query", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::query(...) at test-query.R:11:9
4. └─magmaR:::.query(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-query.R:29:9'): query_df ───────────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-query.R:27:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-query.R:29:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:10:9'): retrieve & retrieveJSON work with minimal input ──
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:9:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(targ, "example", "subject") at test-retrieve.R:10:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:35:9'): retrieve works with targetted input, 1att ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:34:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:35:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:50:9'): retrieve works with targetted input, 1rec ───
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:49:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieve(...) at test-retrieve.R:50:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-retrieve.R:65:9'): retrieveJSON can hide templates ─────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-retrieve.R:64:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveJSON(...) at test-retrieve.R:65:9
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:10:7'): retrieveTemplate ─────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:9:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveTemplate(targ, "example") at test-special.R:10:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:17:7'): retrieveModels ───────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:16:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveModels(targ, "example") at test-special.R:17:7
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:24:7'): retrieveIds ──────────────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:23:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveIds(targ, "example", "subject") at test-special.R:24:7
4. └─magmaR:::.retrieve(...)
5. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:31:7'): retrieveAttributes ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:30:3
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveAttributes(targ, "example", "subject") at test-special.R:31:7
4. └─magmaR::retrieveIds(target, projectName, modelName, ...)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-special.R:38:9'): retrieveParentName ───────────────────────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-special.R:37:5
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveParentName(targ, "example", "demographic") at test-special.R:38:9
4. └─magmaR::retrieveTemplate(target, projectName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
── Error ('test-update.R:12:5'): (code run outside of `test_that()`) ───────────
Error in `.perform_curl_get(fxn = "/retrieve", target, requestBody, parse = TRUE,
verbose = verbose)`: You are unauthorized. Update your 'token' input with 'magmaRset()', then retry.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-update.R:11:1
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") at test-update.R:12:5
4. └─magmaR::retrieveIds(target, projectName, modelName)
5. └─magmaR:::.retrieve(...)
6. └─magmaR:::.perform_curl_get(...)
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64