* using log directory ‘/srv/hornik/tmp/CRAN/CohortAlgebra.Rcheck’ * using R Under development (unstable) (2023-09-10 r85120) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (11) GNU Fortran (Debian 13.2.0-2) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CohortAlgebra/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CohortAlgebra’ version ‘0.0.4’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Gowtham Rao ’ New submission Found the following (possibly) invalid URLs: URL: https://ohdsi.github.io/CohortAlgebra/ From: DESCRIPTION man/CohortAlgebra-package.Rd Status: 404 Message: Not Found * 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 ‘CohortAlgebra’ can be installed ... [3s/3s] 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 files/directories found at top level: ‘cran-comments.md’ ‘man-roxygen’ * 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 ... [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 ... [5s/5s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [4s/106s] ERROR Running ‘testOracle.R’ [0s/0s] Running ‘testPostgres.R’ [2s/2s] Running ‘testRedshift.R’ [0s/0s] Running ‘testSqlServer.R’ [2s/104s] Running the tests in ‘tests/testPostgres.R’ failed. Complete output: > library(testthat) > options(dbms = "postgresql") > test_check("CohortAlgebra") Loading required package: CohortAlgebra 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/RtmpwkCoDi/working_dir/RtmpE4CCxu/jdbcDrivers1928fd2c360621'` 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/RtmpwkCoDi/working_dir/RtmpE4CCxu/jdbcDrivers1928fd2c360621'. [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-copyCohorts.R:31:3'): Testing cohort union ───────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-copyCohorts.R:31:2 2. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 3. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 4. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-deleteCohort.R:34:3'): Testing cohort delete ─────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-deleteCohort.R:34:2 2. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 3. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 4. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-eraFyCohorts.R:52:3'): Testing cohort era fy ─────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-eraFyCohorts.R:52:2 2. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 3. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 4. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-intersectCohorts.R:34:3'): Testing cohort intersect ──────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-intersectCohorts.R:34:2 2. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 3. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 4. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-minusCohorts.R:39:3'): Testing cohort intersect ──────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-minusCohorts.R:39:2 2. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 3. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 4. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-removeOverlappingSubjects.R:26:3'): Testing Remove Subjects from cohorts ── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-removeOverlappingSubjects.R:26:2 2. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 3. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 4. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") ── Error ('test-unionCohorts.R:24:3'): Testing cohort union ──────────────────── Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as / Backtrace: ▆ 1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-unionCohorts.R:24:2 2. └─DatabaseConnector:::connectUsingJdbc(connectionDetails) 3. └─DatabaseConnector:::connectPostgreSql(connectionDetails) 4. └─rlang::abort("Error: database name not included in server string but is required for PostgreSQL. Please specify server as /") [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted Running the tests in ‘tests/testSqlServer.R’ failed. Complete output: > library(testthat) > options(dbms = "sql server") > test_check("CohortAlgebra") Loading required package: CohortAlgebra 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/RtmpwkCoDi/working_dir/Rtmpf4PpOZ/jdbcDrivers19293813bd860f'` 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/RtmpwkCoDi/working_dir/Rtmpf4PpOZ/jdbcDrivers19293813bd860f'. Consider adding `DATABASECONNECTOR_JAR_FOLDER='/tmp/RtmpwkCoDi/working_dir/Rtmpf4PpOZ/jdbcDrivers19293813bd860f'` 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/RtmpwkCoDi/working_dir/Rtmpf4PpOZ/jdbcDrivers19293813bd860f'. [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-copyCohorts.R:31:3'): Testing cohort union ───────────────────── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host localhost, port 1433 has failed. Error: "Connection refused. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.". ── Error ('test-deleteCohort.R:34:3'): Testing cohort delete ─────────────────── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host localhost, port 1433 has failed. Error: "Connection refused. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.". ── Error ('test-eraFyCohorts.R:52:3'): Testing cohort era fy ─────────────────── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host localhost, port 1433 has failed. Error: "Connection refused. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.". ── Error ('test-intersectCohorts.R:34:3'): Testing cohort intersect ──────────── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host localhost, port 1433 has failed. Error: "Connection refused. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.". ── Error ('test-minusCohorts.R:39:3'): Testing cohort intersect ──────────────── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host localhost, port 1433 has failed. Error: "Connection refused. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.". ── Error ('test-removeOverlappingSubjects.R:26:3'): Testing Remove Subjects from cohorts ── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host localhost, port 1433 has failed. Error: "Connection refused. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.". ── Error ('test-unionCohorts.R:24:3'): Testing cohort union ──────────────────── Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: The TCP/IP connection to the host localhost, port 1433 has failed. Error: "Connection refused. Verify the connection properties. Make sure that an instance of SQL Server is running on the host and accepting TCP/IP connections at the port. Make sure that TCP connections to the port are not blocked by a firewall.". [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [0s/0s] OK * checking PDF version of manual ... [3s/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, 2 NOTEs