Last updated on 2022-11-30 08:53:17 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 7.54 | 111.52 | 119.06 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 5.69 | 81.64 | 87.33 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.0 | 258.68 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.0 | 255.31 | OK | |||
| r-devel-windows-x86_64 | 0.3.0 | 80.00 | 227.00 | 307.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 5.99 | 105.58 | 111.57 | ERROR | |
| r-release-linux-x86_64 | 0.1.0 | 5.96 | 97.97 | 103.93 | ERROR | |
| r-release-macos-arm64 | 0.1.0 | 54.00 | NOTE | |||
| r-release-macos-x86_64 | 0.1.0 | 70.00 | NOTE | |||
| r-release-windows-x86_64 | 0.1.0 | 17.00 | 146.00 | 163.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.0 | 62.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 77.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 0.1.0 | 17.00 | 158.00 | 175.00 | ERROR |
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [21s/25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CDMConnector)
>
> test_check("CDMConnector")
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
== Skipped tests ===============================================================
* Sys.getenv("CDM5_POSTGRESQL_USER") == "" is TRUE (2)
* Sys.getenv("CDM5_REDSHIFT_USER") == "" is TRUE (2)
* Sys.getenv("CDM5_SQL_SERVER_USER") == "" is TRUE (2)
* Sys.getenv("LOCAL_POSTGRESQL_USER") == "" is TRUE (2)
== Failed tests ================================================================
-- Error ('test-cdm.R:120'): cdm reference works on duckdb ---------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:120:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-cdm.R:133'): inclusion of cohort tables ------------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:133:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-cdm.R:160'): collect a cdm -------------------------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:160:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-cdm.R:182'): stow and cdm_from_files works ---------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:182:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-dbConnectDetails.R:75'): dbConnectDetails works on duckdb ------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. \-CDMConnector (local) self_contained_query(details, "main") at test-dbConnectDetails.R:75:2
2. +-DBI::dbConnect(connection_details) at test-dbConnectDetails.R:6:2
3. \-DBI::dbConnect(connection_details)
4. \-CDMConnector (local) .local(drv, ...)
5. +-rlang::inject(DBI::dbConnect(!!!l))
6. +-DBI::dbConnect(`<dckdb_dr>`, dbdir = "/tmp/Rtmp2SFfE7/ecbnpgzx/cdm.duckdb")
7. \-DBI::dbConnect(`<dckdb_dr>`, dbdir = "/tmp/Rtmp2SFfE7/ecbnpgzx/cdm.duckdb")
8. \-duckdb (local) .local(drv, ...)
9. \-duckdb::duckdb(dbdir, read_only, bigint, config)
10. +-methods::new(...)
11. | +-methods::initialize(value, ...)
12. | \-methods::initialize(value, ...)
13. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-validate.R:2'): validate cdm works -----------------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-validate.R:2:2
2. \-DBI::dbConnect(duckdb::duckdb(), eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
Error: Test failures
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building 'CDMConnector_and_Dbplyr.Rmd' using rmarkdown
Quitting from lines 33-36 (CDMConnector_and_Dbplyr.Rmd)
Error: processing vignette 'CDMConnector_and_Dbplyr.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'CDMConnector_and_Dbplyr.Rmd'
--- re-building 'DBI_connection_examples.Rmd' using rmarkdown
--- finished re-building 'DBI_connection_examples.Rmd'
--- re-building 'SQL.Rmd' using rmarkdown
--- finished re-building 'SQL.Rmd'
--- re-building 'cdm_reference_backends.Rmd' using rmarkdown
Quitting from lines 40-59 (cdm_reference_backends.Rmd)
Error: processing vignette 'cdm_reference_backends.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'cdm_reference_backends.Rmd'
--- re-building 'getting-started.Rmd' using rmarkdown
Quitting from lines 23-28 (getting-started.Rmd)
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'getting-started.Rmd'
SUMMARY: processing the following files failed:
'CDMConnector_and_Dbplyr.Rmd' 'cdm_reference_backends.Rmd'
'getting-started.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CDMConnector)
>
> test_check("CDMConnector")
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• Sys.getenv("CDM5_POSTGRESQL_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_REDSHIFT_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_SQL_SERVER_USER") == "" is TRUE (2)
• Sys.getenv("LOCAL_POSTGRESQL_USER") == "" is TRUE (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cdm.R:120'): cdm reference works on duckdb ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:120:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:133'): inclusion of cohort tables ────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:133:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:160'): collect a cdm ─────────────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:160:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:182'): stow and cdm_from_files works ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:182:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-dbConnectDetails.R:75'): dbConnectDetails works on duckdb ──────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. └─CDMConnector (local) self_contained_query(details, "main") at test-dbConnectDetails.R:75:2
2. ├─DBI::dbConnect(connection_details) at test-dbConnectDetails.R:6:2
3. └─DBI::dbConnect(connection_details)
4. └─CDMConnector (local) .local(drv, ...)
5. ├─rlang::inject(DBI::dbConnect(!!!l))
6. ├─DBI::dbConnect(`<dckdb_dr>`, dbdir = "/home/hornik/tmp/scratch/RtmpwI3O62/rjmxndgh/cdm.duckdb")
7. └─DBI::dbConnect(`<dckdb_dr>`, dbdir = "/home/hornik/tmp/scratch/RtmpwI3O62/rjmxndgh/cdm.duckdb")
8. └─duckdb (local) .local(drv, ...)
9. └─duckdb::duckdb(dbdir, read_only, bigint, config)
10. ├─methods::new(...)
11. │ ├─methods::initialize(value, ...)
12. │ └─methods::initialize(value, ...)
13. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-validate.R:2'): validate cdm works ─────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-validate.R:2:2
2. └─DBI::dbConnect(duckdb::duckdb(), eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
Error: Test failures
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CDMConnector)
>
> test_check("CDMConnector")
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• Sys.getenv("CDM5_POSTGRESQL_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_REDSHIFT_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_SQL_SERVER_USER") == "" is TRUE (2)
• Sys.getenv("LOCAL_POSTGRESQL_USER") == "" is TRUE (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cdm.R:120'): cdm reference works on duckdb ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:120:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:133'): inclusion of cohort tables ────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:133:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:160'): collect a cdm ─────────────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:160:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:182'): stow and cdm_from_files works ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:182:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-dbConnectDetails.R:75'): dbConnectDetails works on duckdb ──────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. └─CDMConnector (local) self_contained_query(details, "main") at test-dbConnectDetails.R:75:2
2. ├─DBI::dbConnect(connection_details) at test-dbConnectDetails.R:6:2
3. └─DBI::dbConnect(connection_details)
4. └─CDMConnector (local) .local(drv, ...)
5. ├─rlang::inject(DBI::dbConnect(!!!l))
6. ├─DBI::dbConnect(`<dckdb_dr>`, dbdir = "/tmp/RtmpiMst1i/hxwcxkbr/cdm.duckdb")
7. └─DBI::dbConnect(`<dckdb_dr>`, dbdir = "/tmp/RtmpiMst1i/hxwcxkbr/cdm.duckdb")
8. └─duckdb (local) .local(drv, ...)
9. └─duckdb::duckdb(dbdir, read_only, bigint, config)
10. ├─methods::new(...)
11. │ ├─methods::initialize(value, ...)
12. │ └─methods::initialize(value, ...)
13. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-validate.R:2'): validate cdm works ─────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-validate.R:2:2
2. └─DBI::dbConnect(duckdb::duckdb(), eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
Error: Test failures
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Flavor: r-patched-linux-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CDMConnector)
>
> test_check("CDMConnector")
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• Sys.getenv("CDM5_POSTGRESQL_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_REDSHIFT_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_SQL_SERVER_USER") == "" is TRUE (2)
• Sys.getenv("LOCAL_POSTGRESQL_USER") == "" is TRUE (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cdm.R:120'): cdm reference works on duckdb ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:120:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:133'): inclusion of cohort tables ────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:133:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:160'): collect a cdm ─────────────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:160:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:182'): stow and cdm_from_files works ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:182:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-dbConnectDetails.R:75'): dbConnectDetails works on duckdb ──────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. └─CDMConnector (local) self_contained_query(details, "main") at test-dbConnectDetails.R:75:2
2. ├─DBI::dbConnect(connection_details) at test-dbConnectDetails.R:6:2
3. └─DBI::dbConnect(connection_details)
4. └─CDMConnector (local) .local(drv, ...)
5. ├─rlang::inject(DBI::dbConnect(!!!l))
6. ├─DBI::dbConnect(`<dckdb_dr>`, dbdir = "/tmp/RtmpbRNY1u/cfkjsexo/cdm.duckdb")
7. └─DBI::dbConnect(`<dckdb_dr>`, dbdir = "/tmp/RtmpbRNY1u/cfkjsexo/cdm.duckdb")
8. └─duckdb (local) .local(drv, ...)
9. └─duckdb::duckdb(dbdir, read_only, bigint, config)
10. ├─methods::new(...)
11. │ ├─methods::initialize(value, ...)
12. │ └─methods::initialize(value, ...)
13. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-validate.R:2'): validate cdm works ─────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-validate.R:2:2
2. └─DBI::dbConnect(duckdb::duckdb(), eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
Error: Test failures
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Flavor: r-release-linux-x86_64
Version: 0.1.0
Check: installed package size
Result: NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
duckdb 3.8Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CDMConnector)
>
> test_check("CDMConnector")
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• Sys.getenv("CDM5_POSTGRESQL_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_REDSHIFT_USER") == "" is TRUE (2)
• Sys.getenv("CDM5_SQL_SERVER_USER") == "" is TRUE (2)
• Sys.getenv("LOCAL_POSTGRESQL_USER") == "" is TRUE (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cdm.R:120'): cdm reference works on duckdb ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:120:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:133'): inclusion of cohort tables ────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:133:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:160'): collect a cdm ─────────────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:160:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-cdm.R:182'): stow and cdm_from_files works ─────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:182:2
2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-dbConnectDetails.R:75'): dbConnectDetails works on duckdb ──────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. └─CDMConnector (local) self_contained_query(details, "main") at test-dbConnectDetails.R:75:2
2. ├─DBI::dbConnect(connection_details) at test-dbConnectDetails.R:6:2
3. └─DBI::dbConnect(connection_details)
4. └─CDMConnector (local) .local(drv, ...)
5. ├─rlang::inject(DBI::dbConnect(!!!l))
6. ├─DBI::dbConnect(`<dckdb_dr>`, dbdir = "D:\\temp\\RtmpE9YBnj/jgvonauo/cdm.duckdb")
7. └─DBI::dbConnect(`<dckdb_dr>`, dbdir = "D:\\temp\\RtmpE9YBnj/jgvonauo/cdm.duckdb")
8. └─duckdb (local) .local(drv, ...)
9. └─duckdb::duckdb(dbdir, read_only, bigint, config)
10. ├─methods::new(...)
11. │ ├─methods::initialize(value, ...)
12. │ └─methods::initialize(value, ...)
13. └─duckdb:::rapi_startup(dbdir, read_only, config)
── Error ('test-validate.R:2'): validate cdm works ─────────────────────────────
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-validate.R:2:2
2. └─DBI::dbConnect(duckdb::duckdb(), eunomia_dir())
3. └─duckdb (local) .local(drv, ...)
4. └─duckdb::duckdb(dbdir, read_only, bigint, config)
5. ├─methods::new(...)
6. │ ├─methods::initialize(value, ...)
7. │ └─methods::initialize(value, ...)
8. └─duckdb:::rapi_startup(dbdir, read_only, config)
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
Error: Test failures
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Flavor: r-release-windows-x86_64
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'CDMConnector_and_Dbplyr.Rmd' using rmarkdown
Quitting from lines 33-36 (CDMConnector_and_Dbplyr.Rmd)
Error: processing vignette 'CDMConnector_and_Dbplyr.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'CDMConnector_and_Dbplyr.Rmd'
--- re-building 'DBI_connection_examples.Rmd' using rmarkdown
--- finished re-building 'DBI_connection_examples.Rmd'
--- re-building 'SQL.Rmd' using rmarkdown
--- finished re-building 'SQL.Rmd'
--- re-building 'cdm_reference_backends.Rmd' using rmarkdown
Quitting from lines 40-59 (cdm_reference_backends.Rmd)
Error: processing vignette 'cdm_reference_backends.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'cdm_reference_backends.Rmd'
--- re-building 'getting-started.Rmd' using rmarkdown
Quitting from lines 23-28 (getting-started.Rmd)
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'getting-started.Rmd'
SUMMARY: processing the following files failed:
'CDMConnector_and_Dbplyr.Rmd' 'cdm_reference_backends.Rmd'
'getting-started.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CDMConnector)
>
> test_check("CDMConnector")
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
== Skipped tests ===============================================================
* Sys.getenv("CDM5_POSTGRESQL_USER") == "" is TRUE (2)
* Sys.getenv("CDM5_REDSHIFT_USER") == "" is TRUE (2)
* Sys.getenv("CDM5_SQL_SERVER_USER") == "" is TRUE (2)
* Sys.getenv("LOCAL_POSTGRESQL_USER") == "" is TRUE (2)
== Failed tests ================================================================
-- Error ('test-cdm.R:120'): cdm reference works on duckdb ---------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:120:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-cdm.R:133'): inclusion of cohort tables ------------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:133:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-cdm.R:160'): collect a cdm -------------------------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:160:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-cdm.R:182'): stow and cdm_from_files works ---------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-cdm.R:182:2
2. \-DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-dbConnectDetails.R:75'): dbConnectDetails works on duckdb ------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. \-CDMConnector (local) self_contained_query(details, "main") at test-dbConnectDetails.R:75:2
2. +-DBI::dbConnect(connection_details) at test-dbConnectDetails.R:6:2
3. \-DBI::dbConnect(connection_details)
4. \-CDMConnector (local) .local(drv, ...)
5. +-rlang::inject(DBI::dbConnect(!!!l))
6. +-DBI::dbConnect(`<dckdb_dr>`, dbdir = "D:\\temp\\RtmpGiRMJm/uoknxyiz/cdm.duckdb")
7. \-DBI::dbConnect(`<dckdb_dr>`, dbdir = "D:\\temp\\RtmpGiRMJm/uoknxyiz/cdm.duckdb")
8. \-duckdb (local) .local(drv, ...)
9. \-duckdb::duckdb(dbdir, read_only, bigint, config)
10. +-methods::new(...)
11. | +-methods::initialize(value, ...)
12. | \-methods::initialize(value, ...)
13. \-duckdb:::rapi_startup(dbdir, read_only, config)
-- Error ('test-validate.R:2'): validate cdm works -----------------------------
Error: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
Backtrace:
x
1. +-DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-validate.R:2:2
2. \-DBI::dbConnect(duckdb::duckdb(), eunomia_dir())
3. \-duckdb (local) .local(drv, ...)
4. \-duckdb::duckdb(dbdir, read_only, bigint, config)
5. +-methods::new(...)
6. | +-methods::initialize(value, ...)
7. | \-methods::initialize(value, ...)
8. \-duckdb:::rapi_startup(dbdir, read_only, config)
[ FAIL 6 | WARN 0 | SKIP 8 | PASS 5 ]
Error: Test failures
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'CDMConnector_and_Dbplyr.Rmd' using rmarkdown
Quitting from lines 33-36 (CDMConnector_and_Dbplyr.Rmd)
Error: processing vignette 'CDMConnector_and_Dbplyr.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'CDMConnector_and_Dbplyr.Rmd'
--- re-building 'DBI_connection_examples.Rmd' using rmarkdown
--- finished re-building 'DBI_connection_examples.Rmd'
--- re-building 'SQL.Rmd' using rmarkdown
--- finished re-building 'SQL.Rmd'
--- re-building 'cdm_reference_backends.Rmd' using rmarkdown
Quitting from lines 40-59 (cdm_reference_backends.Rmd)
Error: processing vignette 'cdm_reference_backends.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'cdm_reference_backends.Rmd'
--- re-building 'getting-started.Rmd' using rmarkdown
Quitting from lines 23-28 (getting-started.Rmd)
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 38, but we can only read version 39.
The database file was created with an older version of DuckDB.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa.
The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
--- failed re-building 'getting-started.Rmd'
SUMMARY: processing the following files failed:
'CDMConnector_and_Dbplyr.Rmd' 'cdm_reference_backends.Rmd'
'getting-started.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64