* using log directory 'd:/RCompile/CRANincoming/R-devel/CohortAlgebra.Rcheck'
* using R Under development (unstable) (2023-09-10 r85120 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... NOTE
Maintainer: 'Gowtham Rao <rao@ohdsi.org>'

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

Size of tarball: 8513649 bytes
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CohortAlgebra' can be installed ... OK
* checking installed package size ... 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:
  '7576testEunomia.sqlite' 'cran-comments.md' 'man-roxygen' 'sql'
* 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 ... 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 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [109s] ERROR
  Running 'testOracle.R'
  Running 'testPostgres.R'
  Running 'testRedshift.R'
  Running 'testSqlServer.R' [106s]
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='~/.jdbcDrivers'` to C:\Users\CRAN\Documents/.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 'C:\Users\CRAN\Documents/.jdbcDrivers'.
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-copyCohorts.R:30:3'): Testing cohort union ─────────────────────
  Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as <host>/<database>
  Backtrace:
      ▆
   1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-copyCohorts.R:30:2
   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 <host>/<database>")
  ── Error ('test-deleteCohort.R:29:3'): Testing cohort delete ───────────────────
  Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as <host>/<database>
  Backtrace:
      ▆
   1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-deleteCohort.R:29:2
   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 <host>/<database>")
  ── Error ('test-eraFyCohorts.R:50:3'): 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 <host>/<database>
  Backtrace:
      ▆
   1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-eraFyCohorts.R:50:2
   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 <host>/<database>")
  ── Error ('test-intersectCohorts.R:32:3'): Testing cohort intersect ────────────
  Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as <host>/<database>
  Backtrace:
      ▆
   1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-intersectCohorts.R:32:2
   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 <host>/<database>")
  ── Error ('test-minusCohorts.R:36:3'): Testing cohort intersect ────────────────
  Error in `connectPostgreSql(connectionDetails)`: Error: database name not included in server string but is required for PostgreSQL. Please specify server as <host>/<database>
  Backtrace:
      ▆
   1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-minusCohorts.R:36:2
   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 <host>/<database>")
  ── Error ('test-removeOverlappingSubjects.R:21:3'): 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 <host>/<database>
  Backtrace:
      ▆
   1. └─DatabaseConnector::connect(connectionDetails = connectionDetails) at test-removeOverlappingSubjects.R:21:2
   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 <host>/<database>")
  ── 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 <host>/<database>
  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 <host>/<database>")
  
  [ 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='~/.jdbcDrivers'` to C:\Users\CRAN\Documents/.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 'C:\Users\CRAN\Documents/.jdbcDrivers'.
  Consider adding `DATABASECONNECTOR_JAR_FOLDER='~/.jdbcDrivers'` to C:\Users\CRAN\Documents/.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 'C:\Users\CRAN\Documents/.jdbcDrivers'.
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-copyCohorts.R:30:3'): Testing cohort union ─────────────────────
  <SQLServerException/SQLException/Exception/Throwable/Object/error/condition>
  Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", 
      as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: Fehler beim Herstellen der TCP/IP-Verbindung mit dem Host 'localhost', Port 1433. Fehler: 'Connection refused: connect. Überprüfen Sie die Verbindungseigenschaften. Stellen Sie sicher, dass eine SQL Server-Instanz auf dem Host ausgeführt wird und am Port TCP/IP-Verbindungen akzeptiert. Vergewissern Sie sich, dass am Port keine TCP-Verbindungen durch eine Firewall blockiert werden.'.
  ── Error ('test-deleteCohort.R:29:3'): Testing cohort delete ───────────────────
  <SQLServerException/SQLException/Exception/Throwable/Object/error/condition>
  Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", 
      as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: Fehler beim Herstellen der TCP/IP-Verbindung mit dem Host 'localhost', Port 1433. Fehler: 'Connection refused: connect. Überprüfen Sie die Verbindungseigenschaften. Stellen Sie sicher, dass eine SQL Server-Instanz auf dem Host ausgeführt wird und am Port TCP/IP-Verbindungen akzeptiert. Vergewissern Sie sich, dass am Port keine TCP-Verbindungen durch eine Firewall blockiert werden.'.
  ── Error ('test-eraFyCohorts.R:50:3'): Testing cohort era fy ───────────────────
  <SQLServerException/SQLException/Exception/Throwable/Object/error/condition>
  Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", 
      as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: Fehler beim Herstellen der TCP/IP-Verbindung mit dem Host 'localhost', Port 1433. Fehler: 'Connection refused: connect. Überprüfen Sie die Verbindungseigenschaften. Stellen Sie sicher, dass eine SQL Server-Instanz auf dem Host ausgeführt wird und am Port TCP/IP-Verbindungen akzeptiert. Vergewissern Sie sich, dass am Port keine TCP-Verbindungen durch eine Firewall blockiert werden.'.
  ── Error ('test-intersectCohorts.R:32:3'): Testing cohort intersect ────────────
  <SQLServerException/SQLException/Exception/Throwable/Object/error/condition>
  Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", 
      as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: Fehler beim Herstellen der TCP/IP-Verbindung mit dem Host 'localhost', Port 1433. Fehler: 'Connection refused: connect. Überprüfen Sie die Verbindungseigenschaften. Stellen Sie sicher, dass eine SQL Server-Instanz auf dem Host ausgeführt wird und am Port TCP/IP-Verbindungen akzeptiert. Vergewissern Sie sich, dass am Port keine TCP-Verbindungen durch eine Firewall blockiert werden.'.
  ── Error ('test-minusCohorts.R:36:3'): Testing cohort intersect ────────────────
  <SQLServerException/SQLException/Exception/Throwable/Object/error/condition>
  Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", 
      as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: Fehler beim Herstellen der TCP/IP-Verbindung mit dem Host 'localhost', Port 1433. Fehler: 'Connection refused: connect. Überprüfen Sie die Verbindungseigenschaften. Stellen Sie sicher, dass eine SQL Server-Instanz auf dem Host ausgeführt wird und am Port TCP/IP-Verbindungen akzeptiert. Vergewissern Sie sich, dass am Port keine TCP-Verbindungen durch eine Firewall blockiert werden.'.
  ── Error ('test-removeOverlappingSubjects.R:21:3'): Testing Remove Subjects from cohorts ──
  <SQLServerException/SQLException/Exception/Throwable/Object/error/condition>
  Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", 
      as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: Fehler beim Herstellen der TCP/IP-Verbindung mit dem Host 'localhost', Port 1433. Fehler: 'Connection refused: connect. Überprüfen Sie die Verbindungseigenschaften. Stellen Sie sicher, dass eine SQL Server-Instanz auf dem Host ausgeführt wird und am Port TCP/IP-Verbindungen akzeptiert. Vergewissern Sie sich, dass am Port keine TCP-Verbindungen durch eine Firewall blockiert werden.'.
  ── Error ('test-unionCohorts.R:24:3'): Testing cohort union ────────────────────
  <SQLServerException/SQLException/Exception/Throwable/Object/error/condition>
  Error in `rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", 
      as.character(url), p)`: com.microsoft.sqlserver.jdbc.SQLServerException: Fehler beim Herstellen der TCP/IP-Verbindung mit dem Host 'localhost', Port 1433. Fehler: 'Connection refused: connect. Überprüfen Sie die Verbindungseigenschaften. Stellen Sie sicher, dass eine SQL Server-Instanz auf dem Host ausgeführt wird und am Port TCP/IP-Verbindungen akzeptiert. Vergewissern Sie sich, dass am Port keine TCP-Verbindungen durch eine Firewall blockiert werden.'.
  
  [ 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building 'HowToUseCohortAlgebraRPackage.Rmd' using rmarkdown
trying URL 'https://ohdsi.github.io/DatabaseConnectorJars/postgresqlV42.2.18.zip'
Content type 'application/zip' length 931791 bytes (909 KB)
==================================================
downloaded 909 KB


Quitting from lines 95-109 [unnamed-chunk-6] (HowToUseCohortAlgebraRPackage.Rmd)
Error: processing vignette 'HowToUseCohortAlgebraRPackage.Rmd' failed with diagnostics:
Error: database name not included in server string but is required for PostgreSQL. Please specify server as <host>/<database>
--- failed re-building 'HowToUseCohortAlgebraRPackage.Rmd'

SUMMARY: processing the following file failed:
  'HowToUseCohortAlgebraRPackage.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs