• using R Under development (unstable) (2025-11-05 r88988)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘CohortPathways/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘CohortPathways’ version ‘0.0.1’
• 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 ‘CohortPathways’ can be installed ... [14s/50s] OK See the install log for details.
• checking package 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 ... [4s/22s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/15s] OK
• checking whether the package can be unloaded cleanly ... [3s/17s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/14s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/21s] OK
• checking loading without being on the library search path ... [4s/13s] 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 ... [16s/39s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [14s/205s] ERROR   Running ‘testOracle.R’ [4s/68s]   Running ‘testPostgres.R’ [4s/67s]   Running ‘testRedshift.R’   Running ‘testSqlServer.R’ [4s/66s] Running the tests in ‘tests/testOracle.R’ failed. Complete output:   > library(testthat)   > options(dbms = "oracle")   > test_check("CohortPathways")   Loading required package: CohortPathways   Loading required package: DatabaseConnector      Attaching package: 'dplyr'      The following object is masked from 'package:testthat':          matches      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      ************* Testing on oracle *************   Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpbBGImr/working_dir/RtmpQs8FvB/jdbcDrivers1aef5b4a4c8124'` to /data/gannet/ripley/.Renviron and restarting R.   trying URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar'   Error in `FUN()`:   ! In path: "/data/gannet/ripley/R/packages/tests-devel/CohortPathways.Rcheck/tests/testthat/setup.R"   Caused by error in `download.file()`:   ! cannot open URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar'   Backtrace:        ▆     1. ├─testthat::test_check("CohortPathways")     2. │ └─testthat::test_dir(...)     3. │ └─testthat:::test_files(...)     4. │ └─testthat:::test_files_serial(...)     5. │ └─testthat:::test_files_setup_state(...)     6. │ └─testthat::source_test_setup(".", env)     7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)     8. │ └─base::lapply(...)     9. │ └─testthat (local) FUN(X[[i]], ...)    10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)    11. │ ├─base::withCallingHandlers(...)    12. │ └─base::eval(exprs, env)    13. │ └─base::eval(exprs, env)    14. │ └─DatabaseConnector::downloadJdbcDrivers("postgresql", pathToDriver = jdbcDriverFolder) at tests/testthat/setup.R:18:3    15. │ └─utils::download.file(...)    16. └─base::.handleSimpleError(...)    17. └─testthat (local) h(simpleError(msg, call))    18. └─rlang::abort(...)   Warning message:   In download.file(url = paste0(driverSource$baseUrl, driverSource$fileName), :     URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar': Timeout of 60 seconds was reached   Execution halted Running the tests in ‘tests/testPostgres.R’ failed. Complete output:   > library(testthat)   > options(dbms = "postgresql")   > test_check("CohortPathways")   Loading required package: CohortPathways   Loading required package: DatabaseConnector      Attaching package: 'dplyr'      The following object is masked from 'package:testthat':          matches      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      ************* Testing on postgresql *************   Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpbBGImr/working_dir/Rtmp1IFlaB/jdbcDrivers1b1d982e0f51e3'` to /data/gannet/ripley/.Renviron and restarting R.   trying URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar'   Error in `FUN()`:   ! In path: "/data/gannet/ripley/R/packages/tests-devel/CohortPathways.Rcheck/tests/testthat/setup.R"   Caused by error in `download.file()`:   ! cannot open URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar'   Backtrace:        ▆     1. ├─testthat::test_check("CohortPathways")     2. │ └─testthat::test_dir(...)     3. │ └─testthat:::test_files(...)     4. │ └─testthat:::test_files_serial(...)     5. │ └─testthat:::test_files_setup_state(...)     6. │ └─testthat::source_test_setup(".", env)     7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)     8. │ └─base::lapply(...)     9. │ └─testthat (local) FUN(X[[i]], ...)    10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)    11. │ ├─base::withCallingHandlers(...)    12. │ └─base::eval(exprs, env)    13. │ └─base::eval(exprs, env)    14. │ └─DatabaseConnector::downloadJdbcDrivers("postgresql", pathToDriver = jdbcDriverFolder) at tests/testthat/setup.R:18:3    15. │ └─utils::download.file(...)    16. └─base::.handleSimpleError(...)    17. └─testthat (local) h(simpleError(msg, call))    18. └─rlang::abort(...)   Warning message:   In download.file(url = paste0(driverSource$baseUrl, driverSource$fileName), :     URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar': Timeout of 60 seconds was reached   Execution halted Running the tests in ‘tests/testSqlServer.R’ failed. Complete output:   > library(testthat)   > options(dbms = "sql server")   > test_check("CohortPathways")   Loading required package: CohortPathways   Loading required package: DatabaseConnector      Attaching package: 'dplyr'      The following object is masked from 'package:testthat':          matches      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      ************* Testing on sql server *************   Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpbBGImr/working_dir/Rtmp43cyDg/jdbcDrivers1b53df3e7b587d'` to /data/gannet/ripley/.Renviron and restarting R.   trying URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar'   Error in `FUN()`:   ! In path: "/data/gannet/ripley/R/packages/tests-devel/CohortPathways.Rcheck/tests/testthat/setup.R"   Caused by error in `download.file()`:   ! cannot open URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar'   Backtrace:        ▆     1. ├─testthat::test_check("CohortPathways")     2. │ └─testthat::test_dir(...)     3. │ └─testthat:::test_files(...)     4. │ └─testthat:::test_files_serial(...)     5. │ └─testthat:::test_files_setup_state(...)     6. │ └─testthat::source_test_setup(".", env)     7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)     8. │ └─base::lapply(...)     9. │ └─testthat (local) FUN(X[[i]], ...)    10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)    11. │ ├─base::withCallingHandlers(...)    12. │ └─base::eval(exprs, env)    13. │ └─base::eval(exprs, env)    14. │ └─DatabaseConnector::downloadJdbcDrivers("postgresql", pathToDriver = jdbcDriverFolder) at tests/testthat/setup.R:18:3    15. │ └─utils::download.file(...)    16. └─base::.handleSimpleError(...)    17. └─testthat (local) h(simpleError(msg, call))    18. └─rlang::abort(...)   Warning message:   In download.file(url = paste0(driverSource$baseUrl, driverSource$fileName), :     URL 'https://jdbc.postgresql.org/download/postgresql-42.7.3.jar': Timeout of 60 seconds was reached   Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR