* using log directory ‘/Users/ripley/R/packages/tests-devel/SelfControlledCaseSeries.Rcheck’ * using R Under development (unstable) (2026-09-18 r90566) * using platform: aarch64-apple-darwin27.0.0 * R was compiled by Apple clang version 21.0.0 (clang-2100.3.34.2) GNU Fortran (GCC) 14.2.0 * running under: macOS Golden Gate 27.0.1 * using session charset: UTF-8 * current time: 2026-10-10 06:53:35 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘SelfControlledCaseSeries/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SelfControlledCaseSeries’ version ‘6.1.5’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SelfControlledCaseSeries’ can be installed ... [24s/15s] OK * used C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.3.34.2)’ * used SDK: ‘MacOSX27.2.sdk’ * 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 loading without being on the library search path ... 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [32s/34s] [32s/34s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > getOs <- function(){ + sysinf <- Sys.info() + if (!is.null(sysinf)){ + os <- sysinf["sysname"] + if (os == "Darwin") + os <- "mac" + } else { + os <- .Platform$OS.type + if (grepl("^darwin", R.version$os)) + os <- "mac" + if (grepl("linux-gnu", R.version$os)) + os <- "linux" + } + tolower(os) + } > > # Only run linux unit tests in GitHub to avoid weird CRAN flavors where SQLite (EUNOMIA) can be problematic: > if (Sys.getenv("GITHUB_REPOSITORY") != "" || getOs() %in% c("windows", "mac")) { + # Workaround to fix unit tests in check as described here: + # https://github.com/hadley/testthat/issues/86 + Sys.setenv(R_TESTS = "") + + library(testthat) + library(SelfControlledCaseSeries) + test_check("SelfControlledCaseSeries") + } Loading required package: Cyclops Loading required package: DatabaseConnector Loading required package: Andromeda Loading required package: 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 | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | 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'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB Saving _problems/test-eunomia-6.R Initiating cluster with 4 threads | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Stopping cluster | | | 0% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Using 1 thread(s) Model fitting status is: OK Fetched 4 cases from server | | | 0% | |======================================================================| 100% Fetched 3 cases from server | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: Laplace(44.7214) None None None Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Using 1 thread(s) Using 1 thread(s) Warning: BLR gradient is ill-conditioned Enforcing convergence! Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Using 1 thread(s) Warning: BLR gradient is ill-conditioned Enforcing convergence! Warning: BLR gradient is ill-conditioned Enforcing convergence! Using 1 thread(s) Model fitting status is: OK | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================== | 34% | |=============================================== | 67% | |======================================================================| 100% Fitting SCCS model Using prior: None Using 1 thread(s) Using 1 thread(s) Warning: BLR gradient is ill-conditioned Enforcing convergence! Using 1 thread(s) Warning: BLR gradient is ill-conditioned Enforcing convergence! Model fitting status is: OK | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 1 | WARN 1 | SKIP 1 | PASS 244 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-eunomia.R:6:3'): (code run outside of `test_that()`) ─────────── Error: not an error Backtrace: ▆ 1. └─Eunomia::getEunomiaConnectionDetails() at test-eunomia.R:6:3 2. └─Eunomia::getDatabaseFile(...) 3. └─Eunomia::extractLoadData(...) 4. └─Eunomia::loadDataFiles(...) 5. ├─DBI::dbExecute(conn = connection, statement = statement) 6. └─DBI::dbExecute(conn = connection, statement = statement) 7. ├─DBI::dbSendStatement(conn, statement, ...) 8. └─DBI::dbSendStatement(conn, statement, ...) 9. ├─DBI::dbSendQuery(conn, statement, ...) 10. └─RSQLite::dbSendQuery(conn, statement, ...) 11. └─RSQLite (local) .local(conn, statement, ...) 12. ├─methods::new(...) 13. │ ├─methods::initialize(value, ...) 14. │ └─methods::initialize(value, ...) 15. └─RSQLite:::result_create(conn@ptr, statement) [ FAIL 1 | WARN 1 | SKIP 1 | PASS 244 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s/16s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/Users/ripley/R/packages/tests-devel/SelfControlledCaseSeries.Rcheck/00check.log’ for details. 111.68 real 99.18 user 16.33 sys