* using log directory ‘/srv/hornik/tmp/CRAN/ResultModelManager.Rcheck’ * using R Under development (unstable) (2024-07-10 r86888) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (1+b1) Debian flang-new version 18.1.8 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘ResultModelManager/DESCRIPTION’ ... OK * this is package ‘ResultModelManager’ version ‘0.5.9’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Jamie Gilbert ’ New submission Possibly misspelled words in DESCRIPTION: OHDSI (6:59) Found the following (possibly) invalid URLs: URL: https://codecov.io/github/OHDSI/ResultModelManager?branch=main (moved to https://app.codecov.io/github/OHDSI/ResultModelManager?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 ‘ResultModelManager’ can be installed ... [5s/5s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ 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 ... [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/5s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'uploadResults.Rd': ‘generateSqlSchema’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: uploadResults.Rd: generateSqlSchema Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘generateSqlSchema’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [6s/5s] ERROR Running ‘testthat.R’ [6s/5s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ResultModelManager) Loading required package: R6 Loading required package: DatabaseConnector > > test_check("ResultModelManager") Connecting using SQLite driver 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 '/home/hornik/.jdbcDrivers'. Connecting using SQLite driver | | | 0% | |=================================== | 50% | |======================================================================| 100% Executing SQL took 0.00505 secs Connecting using SQLite driver [1] "SELECT 1 * WHERE;" attr(,"sqlDialect") [1] "sqlite" Closing database connection Connecting using SQLite driver Closing database connection Connecting using SQLite driver Closing database connection | | | 0% | |======================================================================| 100% Executing SQL took 0.00285 secs Connecting using SQLite driver | | | 0% | |=================================== | 50% | |======================================================================| 100% Executing SQL took 0.0034 secs Using DatabaseConnector jdbc driver. Initalizing pooled connection Connecting using SQLite driver [1] "SELECT 1 * WHERE;" attr(,"sqlDialect") [1] "sqlite" Initalizing pooled connection Connecting using SQLite driver Initalizing pooled connection Connecting using SQLite driver | | | 0% | |======================================================================| 100% Executing SQL took 0.00283 secs Migrator using SQL files in ResultModelManager Connecting using SQLite driver Creating migrations table Executing SQL took 0.00282 secs Migrations table created Migrator using SQL files in directory structure Connecting using SQLite driver Creating migrations table Executing SQL took 0.00281 secs Migrations table created Migrator using SQL files in directory structure Column databaseId in table foo in results folder foo.zip is of type character, but was expecting bigint. Attempting to convert. Column charField in table foo in results folder foo.zip is of type numeric, but was expecting varchar. Attempting to convert. Column dateField in table foo in results folder foo.zip is of type character, but was expecting date. Attempting to convert. Using DatabaseConnector jdbc driver. Connecting using SQLite driver Connecting using SQLite driver Executing SQL took 0.00337 secs Closing database connection Error in .subset2(e, "finalize")() : attempt to apply non-function Calls: -> In addition: Warning message: call dbDisconnect() when finished working with a connection Connecting using SQLite driver Executing SQL took 0.00296 secs Connecting using SQLite driver Using DatabaseConnector jdbc driver. Initalizing pooled connection Connecting using SQLite driver null/na primary keys found duplicate primary keys found Connecting using SQLite driver Inserting data took 0.0613 secs Connecting using SQLite driver Closing database connection | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Executing SQL took 0.00616 secs Connecting using SQLite driver [ FAIL 6 | WARN 2 | SKIP 7 | PASS 112 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • results db not available (7): 'test-DataModel.R:18:3', 'test-DataModel.R:56:3', 'test-DataModel.R:142:3', 'test-DataModel.R:197:3', 'test-DataModel.R:237:3', 'test-ResultExportManager.R:130:3', 'test-Utils.R:15:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-DataMigrationManager.R:26:3'): Migrations manager runs in package mode ── Check on 'manager$getStatus()' failed: Must have exactly 2 rows, but has 0 rows Backtrace: ▆ 1. └─checkmate::expect_data_frame(manager$getStatus(), nrows = 2) at test-DataMigrationManager.R:26:3 2. └─checkmate::makeExpectation(x, res, info, label) ── Failure ('test-DataMigrationManager.R:27:3'): Migrations manager runs in package mode ── all(manager$getStatus()$executed) is not FALSE `actual`: TRUE `expected`: FALSE ── Error ('test-DataMigrationManager.R:28:3'): Migrations manager runs in package mode ── Error in `!migrations$executed`: invalid argument type Backtrace: ▆ 1. └─manager$executeMigrations() at test-DataMigrationManager.R:28:3 2. ├─migrations[!migrations$executed, ] 3. └─base::`[.data.frame`(migrations, !migrations$executed, ) ── Error ('test-DataMigrationManager.R:60:3'): Migrations manager runs in folder mode ── Error in `!migrations$executed`: invalid argument type Backtrace: ▆ 1. └─manager$executeMigrations() at test-DataMigrationManager.R:60:3 2. ├─migrations[!migrations$executed, ] 3. └─base::`[.data.frame`(migrations, !migrations$executed, ) ── Error ('test-DataMigrationManager.R:70:3'): Add migration and execute ─────── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. └─base::write(...) at test-DataMigrationManager.R:70:3 2. └─base::cat(...) 3. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test-DataMigrationManager.R:91:3'): Add invalid filename ──────────── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. └─base::write("", file.path("migrations", "sql_server", "foo.sql")) at test-DataMigrationManager.R:91:3 2. └─base::cat(...) 3. └─base::file(file, ifelse(append, "a", "w")) [ FAIL 6 | WARN 2 | SKIP 7 | PASS 112 ] Error: Test failures Execution halted Closing database connection * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s/15s] 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 WARNINGs, 1 NOTE