Last updated on 2025-02-24 19:50:45 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.4 | 4.04 | 77.87 | 81.91 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.4 | 2.80 | 59.34 | 62.14 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.4 | 126.52 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.4 | 145.14 | ERROR | |||
| r-devel-macos-arm64 | 2.1.4 | 51.00 | OK | |||
| r-devel-macos-x86_64 | 2.1.4 | 96.00 | OK | |||
| r-devel-windows-x86_64 | 2.1.4 | 6.00 | 170.00 | 176.00 | OK | |
| r-patched-linux-x86_64 | 2.1.4 | 10.74 | 73.80 | 84.54 | OK | |
| r-release-linux-x86_64 | 2.1.4 | 3.73 | 74.64 | 78.37 | OK | |
| r-release-macos-arm64 | 2.1.4 | 59.00 | OK | |||
| r-release-macos-x86_64 | 2.1.4 | 74.00 | OK | |||
| r-release-windows-x86_64 | 2.1.4 | 7.00 | 167.00 | 174.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.4 | 53.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.1.4 | 101.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.1.4 | 8.00 | 185.00 | 193.00 | ERROR |
Version: 2.1.4
Check: tests
Result: ERROR
Running ‘test-all.R’ [20s/30s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("restez")
Loading required package: restez
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Inspecting 1 file(s) to add to the database ...
... 'test.seq.gz' (1/1)
Done.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Inspecting 1 file(s) to add to the database ...
... 'test.seq.gz' (1/1)
Done.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Looking up latest GenBank release ...
... release number 1000
... found 1 sequence files
────────────────────────────────────────────────────────────────────────────────
Which sequence file types would you like to download?
Choose from those listed below:
• 1 - 'type1'
1 files and 1e-07 GB
Provide one or more numbers separated by spaces.
e.g. to download all Mammalian sequences, type: "" followed by Enter
Which files would you like to download?
────────────────────────────────────────────────────────────────────────────────
You've selected a total of 1 file(s) and 1e-07 GB of uncompressed data.
These represent:
• 'type1'
Based on stated GenBank files sizes, we estimate ...
... 2e-08 GB for compressed, downloaded files
... 1.22e-07 GB for the SQL database
Leading to a total of 1.42e-07 GB
Please note, the real sizes of the database and its downloads cannot be
accurately predicted beforehand.
These are just estimates, actual sizes may differ by up to a factor of two.
Is this OK?
────────────────────────────────────────────────────────────────────────────────
Downloading ...
... 'file1.seq' (1/1)
Done. Enjoy your day.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... '1' (1/10)
... ... Hmmmm... no records found in that file.
... '2' (2/10)
... ... Hmmmm... no records found in that file.
... '3' (3/10)
... ... Hmmmm... no records found in that file.
... '4' (4/10)
... ... Hmmmm... no records found in that file.
... '5' (5/10)
... ... Hmmmm... no records found in that file.
... '6' (6/10)
... ... Hmmmm... no records found in that file.
... '7' (7/10)
... ... Hmmmm... no records found in that file.
... '8' (8/10)
... ... Hmmmm... no records found in that file.
... '9' (9/10)
... ... Hmmmm... no records found in that file.
... '10' (10/10)
... ... Hmmmm... no records found in that file.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... ... Your database is out-of-date. Latest release is 256
... ... Your database is up-to-date
example text example text'example text'example text
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'Yes'
... Total size 780K
... Does the database have data? 'Yes'
... Number of sequences 10
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 138 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-db-tools.R:138:3'
• On Linux (1): 'test-db-tools.R:79:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get-tools.R:36:3'): gb_sequence_get() works ──────────────────
names(seq_dnabin_2) not equal to `id_2`.
2/2 mismatches
x[1]: "AC092035"
y[1]: "AC091545"
x[2]: "AC091545"
y[2]: "AC092035"
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 138 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.4
Check: tests
Result: ERROR
Running ‘test-all.R’ [34s/64s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("restez")
Loading required package: restez
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Looking up latest GenBank release ...
... release number 1000
... found 1 sequence files
────────────────────────────────────────────────────────────────────────────────
Which sequence file types would you like to download?
Choose from those listed below:
• 1 - 'type1'
1 files and 1e-07 GB
Provide one or more numbers separated by spaces.
e.g. to download all Mammalian sequences, type: "" followed by Enter
Which files would you like to download?
────────────────────────────────────────────────────────────────────────────────
You've selected a total of 1 file(s) and 1e-07 GB of uncompressed data.
These represent:
• 'type1'
Based on stated GenBank files sizes, we estimate ...
... 2e-08 GB for compressed, downloaded files
... 1.22e-07 GB for the SQL database
Leading to a total of 1.42e-07 GB
Please note, the real sizes of the database and its downloads cannot be
accurately predicted beforehand.
These are just estimates, actual sizes may differ by up to a factor of two.
Is this OK?
────────────────────────────────────────────────────────────────────────────────
Downloading ...
... 'file1.seq' (1/1)
Done. Enjoy your day.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... '1' (1/10)
... ... Hmmmm... no records found in that file.
... '2' (2/10)
... ... Hmmmm... no records found in that file.
... '3' (3/10)
... ... Hmmmm... no records found in that file.
... '4' (4/10)
... ... Hmmmm... no records found in that file.
... '5' (5/10)
... ... Hmmmm... no records found in that file.
... '6' (6/10)
... ... Hmmmm... no records found in that file.
... '7' (7/10)
... ... Hmmmm... no records found in that file.
... '8' (8/10)
... ... Hmmmm... no records found in that file.
... '9' (9/10)
... ... Hmmmm... no records found in that file.
... '10' (10/10)
... ... Hmmmm... no records found in that file.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... ... Your database is out-of-date. Latest release is 256
... ... Your database is up-to-date
example text example text'example text'example text
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'Yes'
... Total size 780K
... Does the database have data? 'Yes'
... Number of sequences 10
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
[ FAIL 5 | WARN 1 | SKIP 1 | PASS 121 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-db-tools.R:138:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-db-tools.R:32:3'): db_create() works ───────────────────────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:32:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
── Error ('test-db-tools.R:43:3'): search_gz() works ───────────────────────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:43:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
── Error ('test-db-tools.R:60:3'): search_gz() works inside db_create() ────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:60:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
── Error ('test-db-tools.R:77:3'): search_gz() warning works ───────────────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:77:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
── Error ('test-entrez-tools.R:17:1'): (code run outside of `test_that()`) ─────
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query
Error: Catalog Error: Table with name "nucleotide" already exists!
Backtrace:
▆
1. ├─restez:::gb_sql_add(df = df) at test-entrez-tools.R:17:1
2. │ ├─DBI::dbExecute(conn = connection, "CREATE TABLE nucleotide (\n accession VARCHAR(20),\n version INT,\n organism VARCHAR(100),\n raw_definition VARCHAR,\n raw_sequence VARCHAR,\n raw_record VARCHAR,\n PRIMARY KEY (accession)\n )")
3. │ └─DBI::dbExecute(conn = connection, "CREATE TABLE nucleotide (\n accession VARCHAR(20),\n version INT,\n organism VARCHAR(100),\n raw_definition VARCHAR,\n raw_sequence VARCHAR,\n raw_record VARCHAR,\n PRIMARY KEY (accession)\n )")
4. │ ├─DBI::dbSendStatement(conn, statement, ...)
5. │ └─DBI::dbSendStatement(conn, statement, ...)
6. │ ├─DBI::dbSendQuery(conn, statement, ...)
7. │ └─duckdb::dbSendQuery(conn, statement, ...)
8. │ └─duckdb (local) .local(conn, statement, ...)
9. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
10. │ └─duckdb:::duckdb_execute(res)
11. │ └─duckdb:::rethrow_rapi_execute(...)
12. │ ├─rlang::try_fetch(...)
13. │ │ ├─base::tryCatch(...)
14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─duckdb:::rapi_execute(stmt, arrow, integer64)
19. └─base::.handleSimpleError(...)
20. └─rlang (local) h(simpleError(msg, call))
21. └─handlers[[1L]](cnd)
22. └─duckdb:::rethrow_error_from_rapi(e, call)
23. └─rlang::abort(msg, call = call)
[ FAIL 5 | WARN 1 | SKIP 1 | PASS 121 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.1.4
Check: tests
Result: ERROR
Running ‘test-all.R’ [55s/112s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("restez")
Loading required package: restez
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Looking up latest GenBank release ...
... release number 1000
... found 1 sequence files
────────────────────────────────────────────────────────────────────────────────
Which sequence file types would you like to download?
Choose from those listed below:
• 1 - 'type1'
1 files and 1e-07 GB
Provide one or more numbers separated by spaces.
e.g. to download all Mammalian sequences, type: "" followed by Enter
Which files would you like to download?
────────────────────────────────────────────────────────────────────────────────
You've selected a total of 1 file(s) and 1e-07 GB of uncompressed data.
These represent:
• 'type1'
Based on stated GenBank files sizes, we estimate ...
... 2e-08 GB for compressed, downloaded files
... 1.22e-07 GB for the SQL database
Leading to a total of 1.42e-07 GB
Please note, the real sizes of the database and its downloads cannot be
accurately predicted beforehand.
These are just estimates, actual sizes may differ by up to a factor of two.
Is this OK?
────────────────────────────────────────────────────────────────────────────────
Downloading ...
... 'file1.seq' (1/1)
Done. Enjoy your day.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... '1' (1/10)
... ... Hmmmm... no records found in that file.
... '2' (2/10)
... ... Hmmmm... no records found in that file.
... '3' (3/10)
... ... Hmmmm... no records found in that file.
... '4' (4/10)
... ... Hmmmm... no records found in that file.
... '5' (5/10)
... ... Hmmmm... no records found in that file.
... '6' (6/10)
... ... Hmmmm... no records found in that file.
... '7' (7/10)
... ... Hmmmm... no records found in that file.
... '8' (8/10)
... ... Hmmmm... no records found in that file.
... '9' (9/10)
... ... Hmmmm... no records found in that file.
... '10' (10/10)
... ... Hmmmm... no records found in that file.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... ... Your database is out-of-date. Latest release is 256
... ... Your database is up-to-date
example text example text'example text'example text
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'Yes'
... Total size 780K
... Does the database have data? 'Yes'
... Number of sequences 10
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
[ FAIL 4 | WARN 1 | SKIP 1 | PASS 133 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-db-tools.R:138:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-db-tools.R:32:3'): db_create() works ───────────────────────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:32:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
── Error ('test-db-tools.R:43:3'): search_gz() works ───────────────────────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:43:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
── Error ('test-db-tools.R:60:3'): search_gz() works inside db_create() ────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:60:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
── Error ('test-db-tools.R:77:3'): search_gz() warning works ───────────────────
Error in `regexpr(as.character(pattern), text, ignore.case, perl, fixed,
useBytes)`: NA in coercion to Rboolean
Backtrace:
▆
1. ├─R.utils::gzip(fp) at test-db-tools.R:77:3
2. └─R.utils::gzip.default(fp)
3. ├─R.utils::compressFile(filename = filename, ..., ext = ext, FUN = FUN)
4. └─R.utils::compressFile.default(...)
5. ├─R.utils::popTemporaryFile(destnameT)
6. └─R.utils::popTemporaryFile.default(destnameT)
7. └─base::regexpr(pattern, "", pathnameT)
[ FAIL 4 | WARN 1 | SKIP 1 | PASS 133 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.1.4
Check: tests
Result: ERROR
Running 'test-all.R' [73s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
> library(testthat)
> test_check("restez")
Loading required package: restez
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf8564c68e7". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf860cd7839". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf847c6290d". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf8218a639c". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf83e5e7ddb". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf8934465". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf8763d6cc0". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf82af17e0a". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf865d14f89". Did you mean command "preview"?
Inspecting 1 file(s) to add to the database ...
... 'test.seq.gz' (1/1)
Done.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf841c42f0d". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf8463b431e". Did you mean command "preview"?
Inspecting 1 file(s) to add to the database ...
... 'test.seq.gz' (1/1)
Done.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf860e64177". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf845057e0b". Did you mean command "preview"?
────────────────────────────────────────────────────────────────────────────────
Looking up latest GenBank release ...
... release number 1000
... found 1 sequence files
────────────────────────────────────────────────────────────────────────────────
Which sequence file types would you like to download?
Choose from those listed below:
• 1 - 'type1'
1 files and 1e-07 GB
Provide one or more numbers separated by spaces.
e.g. to download all Mammalian sequences, type: "" followed by Enter
Which files would you like to download?
────────────────────────────────────────────────────────────────────────────────
You've selected a total of 1 file(s) and 1e-07 GB of uncompressed data.
These represent:
• 'type1'
Based on stated GenBank files sizes, we estimate ...
... 2e-08 GB for compressed, downloaded files
... 1.22e-07 GB for the SQL database
Leading to a total of 1.42e-07 GB
Please note, the real sizes of the database and its downloads cannot be
accurately predicted beforehand.
These are just estimates, actual sizes may differ by up to a factor of two.
Is this OK?
────────────────────────────────────────────────────────────────────────────────
Downloading ...
... 'file1.seq' (1/1)
Done. Enjoy your day.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf827371a8". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf84be73d0c". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf82ff0554d". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf871c51f64". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf8436e24be". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf83d106c6d". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf87c5d645c". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf838832350". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf860dc6962". Did you mean command "preview"?
... '1' (1/10)
... ... Hmmmm... no records found in that file.
... '2' (2/10)
... ... Hmmmm... no records found in that file.
... '3' (3/10)
... ... Hmmmm... no records found in that file.
... '4' (4/10)
... ... Hmmmm... no records found in that file.
... '5' (5/10)
... ... Hmmmm... no records found in that file.
... '6' (6/10)
... ... Hmmmm... no records found in that file.
... '7' (7/10)
... ... Hmmmm... no records found in that file.
... '8' (8/10)
... ... Hmmmm... no records found in that file.
... '9' (9/10)
... ... Hmmmm... no records found in that file.
... '10' (10/10)
... ... Hmmmm... no records found in that file.
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf87ac32651". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf861cd2ce". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf8134a855". Did you mean command "preview"?
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf831c5103a". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf84b696de5". Did you mean command "render"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf870774679". Did you mean command "preview"?
... ... Your database is out-of-date. Latest release is 256
... ... Your database is up-to-date
example text example text'example text'example text
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf827b02282". Did you mean command "preview"?
Checking setup status at ...
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf86e2b4fea". Did you mean command "preview"?
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'Yes'
... Total size 780K
... Does the database have data? 'Yes'
... Number of sequences 10
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf870b64fe0". Did you mean command "preview"?
... Creating 'test_db_fldr/restez'
... Creating 'test_db_fldr/restez/downloads'
ERROR: Unknown command "TMPDIR=D:/temp/2025_02_21_01_50_00_1228/RtmpaeQVrE/file20cf82a83de6". Did you mean command "render"?
────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path 'test_db_fldr/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────
Download ...
... Path 'test_db_fldr/restez/downloads'
... Does path exist? 'Yes'
... N. files 0
... Total size 0
... GenBank division selections ''
... GenBank Release '0'
... Last updated ''
────────────────────────────────────────────────────────────────────────────────
Database ...
... Path 'test_db_fldr/restez/sql_db'
... Does path exist? 'No'
... Total size NA
... Does the database have data? 'No'
... Number of sequences 0
... Min. sequence length '0'
... Max. sequence length 'Inf'
... Last_updated ''
[ FAIL 1 | WARN 34 | SKIP 3 | PASS 135 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-db-tools.R:138:3'
• On Windows (2): 'test-db-tools.R:45:3', 'test-db-tools.R:62:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get-tools.R:36:3'): gb_sequence_get() works ──────────────────
names(seq_dnabin_2) not equal to `id_2`.
2/2 mismatches
x[1]: "KBQR00000000"
y[1]: "AC090337"
x[2]: "AC090337"
y[2]: "KBQR00000000"
[ FAIL 1 | WARN 34 | SKIP 3 | PASS 135 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64