* 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 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 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