* using log directory ‘/srv/hornik/tmp/CRAN/CommonDataModel.Rcheck’ * using R Under development (unstable) (2024-01-29 r85841) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CommonDataModel/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CommonDataModel’ version ‘0.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Clair Blacketer ’ New submission Possibly misspelled words in DESCRIPTION: CDM (3:13) DDL (3:17, 7:86, 7:186) OHDSql (7:64, 7:208) OMOP (3:8) SqlRender (7:153) csv (7:41) Package has a VignetteBuilder field but no prebuilt vignette index. The Description field should not start with the package name, 'This package' or similar. * 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 serialization versions ... OK * checking whether package ‘CommonDataModel’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘output’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/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 ... [2s/2s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) listSupportedVersions.Rd:10: Lost braces; missing escapes or markup? 10 | A character vector containing the support CDM versions in {major}.{minor} format. | ^ checkRd: (-1) listSupportedVersions.Rd:10: Lost braces; missing escapes or markup? 10 | A character vector containing the support CDM versions in {major}.{minor} format. | ^ * 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 ... [0s/0s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [14s/18s] ERROR Running ‘testthat.R’ [14s/18s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CommonDataModel) > > test_check("CommonDataModel") DATABASECONNECTOR_JAR_FOLDER environment variable is empty string downloading drivers Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'` to /home/hornik/.Renviron and restarting R. trying URL 'https://s3.amazonaws.com/redshift-downloads/drivers/jdbc/2.1.0.20/redshift-jdbc42-2.1.0.20.zip' Content type 'application/zip' length 8434563 bytes (8.0 MB) ================================================== downloaded 8.0 MB DatabaseConnector redshift JDBC driver downloaded to '/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'` to /home/hornik/.Renviron and restarting R. trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/postgresqlV42.2.18.zip' Content type 'application/zip' length 931791 bytes (909 KB) ================================================== downloaded 909 KB DatabaseConnector postgresql JDBC driver downloaded to '/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'` to /home/hornik/.Renviron and restarting R. trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/oracleV19.8.zip' Content type 'application/zip' length 4101479 bytes (3.9 MB) ================================================== downloaded 3.9 MB DatabaseConnector oracle JDBC driver downloaded to '/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'` to /home/hornik/.Renviron and restarting R. trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/sqlServerV9.2.0.zip' Content type 'application/zip' length 1262814 bytes (1.2 MB) ================================================== downloaded 1.2 MB DatabaseConnector sql server JDBC driver downloaded to '/tmp/Rtmp1yja2S/working_dir/RtmpXjNtg1'. Connecting using PostgreSQL driver Connecting using PostgreSQL driver Connecting using PostgreSQL driver [ FAIL 5 | WARN 0 | SKIP 0 | PASS 31 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-buildRelease.R:28:3'): buildRelease() output matches current ddl folder ── `generatedChecksums` (`actual`) and `currentChecksums` (`expected`) don't have the same values. * Only in `expected`: "631ee4b2c3036b36c4a0bf31eb8cdc71", "35794f90df6ca8e23b276830be464147", "bbb3732a5ad1329c1431e61a7b4fee4c", "24513ba3e9cd540cb81fb3a9c251cbd2", "60afdf083f42d01efc87ab5fbb8ef025", "f146cc01720a26c74aa1d0b40c3d2b28" * Only in `actual`: "7851a38d2fa642fdd711e27bc4c2e02e", "9a6326798aaa8e74945e607d12ea671c", "0b782539cebf6afc914659d52cc7f319", "379d1346232cfe178ffe5c4700745044", "5681fcf6588ba6b1f54b3c8ffeee31cc", "e8dcf670cb373d461e5ea994c9aaaea1" ── Failure ('test-executeDdl.R:19:5'): Can connect to postgresql ─────────────── `con <- connect(connectionDetails)` threw an unexpected error. Message: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Class: rlang_error/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(con <- connect(connectionDetails), NA) at test-executeDdl.R:19:5 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─DatabaseConnector::connect(connectionDetails) 8. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 9. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 10. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Failure ('test-executeDdl.R:20:5'): Can connect to postgresql ─────────────── `disconnect(con)` threw an unexpected error. Message: object 'con' not found Class: simpleError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(disconnect(con), NA) at test-executeDdl.R:20:5 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─DatabaseConnector::disconnect(con) ── Error ('test-executeDdl.R:26:7'): DDL 5.3 runs on postgresql ──────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─CommonDataModel:::dropAllTablesFromSchema(...) at test-executeDdl.R:26:7 2. └─CommonDataModel:::listTablesInSchema(connectionDetails, schema) at tests/testthat/setup.R:99:3 3. └─DatabaseConnector::connect(connectionDetails) at tests/testthat/setup.R:84:3 4. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 5. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 6. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-executeDdl.R:26:7'): DDL 5.4 runs on postgresql ──────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─CommonDataModel:::dropAllTablesFromSchema(...) at test-executeDdl.R:26:7 2. └─CommonDataModel:::listTablesInSchema(connectionDetails, schema) at tests/testthat/setup.R:99:3 3. └─DatabaseConnector::connect(connectionDetails) at tests/testthat/setup.R:84:3 4. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 5. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 6. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") [ FAIL 5 | WARN 0 | SKIP 0 | PASS 31 ] Error: Test failures Execution halted * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 3 NOTEs