* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CohortGenerator.Rcheck’ * using R Under development (unstable) (2024-09-03 r87093) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CohortGenerator/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CohortGenerator’ version ‘0.11.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Anthony Sena ’ New submission Possibly misspelled words in DESCRIPTION: CDM (3:60, 14:103) OMOP (3:55, 14:98) Found the following (possibly) invalid URLs: URL: https://codecov.io/github/OHDSI/CohortGenerator?branch=main (moved to https://app.codecov.io/github/OHDSI/CohortGenerator?branch=main) From: README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 ‘CohortGenerator’ can be installed ... [7s/7s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘errorReportSql.txt’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [6s/6s] OK * checking Rd files ... [0s/0s] 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [51s/39s] ERROR Running ‘testthat.R’ [51s/39s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CohortGenerator) Loading required package: DatabaseConnector Loading required package: R6 > > test_check("CohortGenerator") attempting to download GiBleed trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB attempting to extract and load: /tmp/RtmpAUrzwq/working_dir/RtmpLLMuqN/GiBleed_5.3.zip to: /tmp/RtmpAUrzwq/working_dir/RtmpLLMuqN/GiBleed_5.3.sqlite Initiating cluster consisting only of main thread Generating cohort set took 0.65 secs Initiating cluster consisting only of main thread Generating cohort set took 0.43 secs Initiating cluster consisting only of main thread Generating cohort set took 0.03 secs Initiating cluster consisting only of main thread Generating cohort set took 0.25 secs Initiating cluster consisting only of main thread Generating cohort set took 0.29 secs Initiating cluster consisting only of main thread Generating cohort set took 0.03 secs Initiating cluster consisting only of main thread An error occurred while generating cohortName = Fail Cohort. Error: Error in `.createErrorReport()`: ! Error executing SQL: no such table: main.non_existant_table An error report has been created at /srv/hornik/tmp/CRAN_pretest/CohortGenerator.Rcheck/tests/testthat/errorReportSql.txt [1] "Create cohorts with stopOnError = FALSE" Initiating cluster consisting only of main thread An error occurred while generating cohortName = Fail Cohort. Error: Error in `.createErrorReport()`: ! Error executing SQL: no such table: main.non_existant_table An error report has been created at /srv/hornik/tmp/CRAN_pretest/CohortGenerator.Rcheck/tests/testthat/errorReportSql.txt Generating cohort set took 0.3 secs Initiating cluster consisting only of main thread An error occurred while generating cohortName = Fail Cohort. Error: Error in `.createErrorReport()`: ! Error executing SQL: no such table: main.non_existant_table An error report has been created at /srv/hornik/tmp/CRAN_pretest/CohortGenerator.Rcheck/tests/testthat/errorReportSql.txt Generating cohort set took 0.31 secs Initiating cluster consisting only of main thread Generating cohort set took 0.05 secs trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB Cohorts created in table main.cohort trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB Initiating cluster consisting only of main thread Generating cohort set took 0.29 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Generating sample set took 0.24 secs Generating sample set took 0.03 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Generating sample set took 0.17 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Initiating cluster consisting only of main thread Generating cohort set took 0.34 secs Initiating cluster consisting only of main thread Generating cohort set took 0.35 secs Initiating cluster consisting only of main thread Generating cohort set took 0.33 secs Initiating cluster consisting only of main thread Generating cohort set took 0.33 secs Initiating cluster consisting only of main thread Generating cohort set took 0.33 secs Initiating cluster consisting only of main thread Generating cohort set took 0.33 secs Generating negative control outcomes set took 0.04 secs Generating negative control outcomes set took 0.03 secs Negative control set skipped Generating negative control outcomes set took 0.04 secs Negative control set skipped Generating negative control outcomes set took 0.03 secs Negative control set skipped trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/postgresqlV42.2.18.zip' Content type 'application/zip' length 931791 bytes (909 KB) ================================================== downloaded 909 KB Initiating cluster consisting only of main thread Generating cohort set took 0.33 secs Generating negative control outcomes set took 0.03 secs Initiating cluster consisting only of main thread Generating cohort set took 0.33 secs Generating negative control outcomes set took 0.03 secs Initiating cluster consisting only of main thread Generating cohort set took 0.32 secs Generating negative control outcomes set took 0.03 secs Initiating cluster consisting only of main thread Generating cohort set took 0.43 secs Initiating cluster consisting only of main thread Generating cohort set took 0.06 secs Initiating cluster consisting only of main thread Generating cohort set took 0.4 secs [1] "No platform details available for bigquery" trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/oracleV19.8.zip' Content type 'application/zip' length 4101479 bytes (3.9 MB) ================================================== downloaded 3.9 MB [1] "Testing oracle" Error in rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", : java.sql.SQLRecoverableException: IO Error: The Network Adapter could not establish the connection In addition: Warning message: call dbDisconnect() when finished working with a connection Error in rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", : java.sql.SQLRecoverableException: IO Error: The Network Adapter could not establish the connection [ FAIL 4 | WARN 0 | SKIP 0 | PASS 405 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-ResultsDataModel.R:84:3'): Create schema ─────────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─CohortGenerator (local) testCreateSchema(...) at test-ResultsDataModel.R:84:3 2. └─DatabaseConnector::connect(connectionDetails) at test-ResultsDataModel.R:52:3 3. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 4. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 5. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-ResultsDataModel.R:140:3'): Results upload ───────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─CohortGenerator (local) testUploadResults(...) at test-ResultsDataModel.R:140:3 2. └─CohortGenerator::uploadResults(...) at test-ResultsDataModel.R:95:3 3. └─ResultModelManager::uploadResults(...) 4. └─DatabaseConnector::connect(connectionDetails) 5. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 6. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 7. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-dbms-platforms.R:97:7'): platform specific create cohorts with stats, Incremental, get results ── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: java.sql.SQLRecoverableException: IO Error: Connect identifier was empty. ── Error ('test-dbms-platforms.R:97:7'): platform specific create cohorts with stats, Incremental, get results ── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: java.sql.SQLRecoverableException: IO Error: Connect identifier was empty. [ FAIL 4 | WARN 0 | SKIP 0 | PASS 405 ] Error: Test failures Connecting using PostgreSQL driver Error in `connectPostgreSql()`: ! Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. ├─testthat::test_check("CohortGenerator") 2. │ └─testthat::test_dir(...) 3. │ └─testthat:::test_files(...) 4. │ └─testthat:::test_files_serial(...) 5. │ └─withr (local) ``() 6. └─DatabaseConnector::connect(connectionDetails = postgresConnectionDetails) at test-ResultsDataModel.R:37:5 7. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 8. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 9. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [22s/17s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs