• 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 See the install log for details.
• 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