Running ‘test-all.R’ [38s/86s]
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]: "AC090337"
  y[1]: "NR_040059"
  
  x[2]: "NR_040059"
  y[2]: "AC090337"
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 138 ]
  Error: Test failures
  Execution halted