* using log directory 'd:/Rcompile/CRANpkg/local/4.6/magmaR.Rcheck'
* using R Under development (unstable) (2025-07-21 r88439 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'magmaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'magmaR' version '1.0.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 whether package 'magmaR' 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 ... [0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s] OK
* checking loading without being on the library search path ... [0s] OK
* checking use of S3 registration ... 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 ... [3s] OK
* checking Rd files ... [1s] 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [1s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [10s] 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8s] 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

* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... [3s] OK
* DONE
Status: 2 ERRORs