Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pmparser)
  > 
  > test_check('pmparser')
  [ FAIL 26 | WARN 4 | SKIP 4 | PASS 103 ]
  
  == Skipped tests ===============================================================
  * On CRAN (4)
  
  == Failed tests ================================================================
  -- Error ('test_modify_pubmed_db_dup.R:51'): modifyPubmedDb create is unique ---
  Error in `gzfile(file, open = "rb")`: cannot open the connection
  Backtrace:
      x
   1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:2
   2.   \-pmparser::getCitation(...)
   3.     \-pmparser:::writeTableInChunks(...)
   4.       +-R.utils::countLines(path)
   5.       \-R.utils::countLines.default(path)
   6.         \-base::gzfile(file, open = "rb")
  -- Error ('test_modify_pubmed_db_std.R:22'): modifyPubmedDb create matches standard --
  Error in `gzfile(file, open = "rb")`: cannot open the connection
  Backtrace:
      x
   1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:2
   2.   \-pmparser::getCitation(...)
   3.     \-pmparser:::writeTableInChunks(...)
   4.       +-R.utils::countLines(path)
   5.       \-R.utils::countLines.default(path)
   6.         \-base::gzfile(file, open = "rb")
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (57, 117) differ >
  Component "pmid": Numeric: lengths (57, 117) differ
  Component "text": Lengths (57, 117) differ (string compare on first 57)
  Component "label": Lengths (57, 117) differ (string compare on first 57)
  Component "nlm_category": Lengths (57, 117) differ (string compare on first 57)
  Component "abstract_pos": Numeric: lengths (57, 117) differ
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (19, 34) differ >
  Component "pmid": Numeric: lengths (19, 34) differ
  Component "copyright": Lengths (19, 34) differ (string compare on first 19)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  article not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
  Component "pmid": Numeric: lengths (28, 58) differ
  Component "title": Lengths (28, 58) differ (string compare on first 28)
  Component "pub_date": Numeric: lengths (28, 58) differ
  Component "pub_model": Lengths (28, 58) differ (string compare on first 28)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  article_id not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (38, 76) differ >
  Component "pmid": Numeric: lengths (38, 76) differ
  Component "id_type": Lengths (38, 76) differ (string compare on first 38)
  Component "id_value": Lengths (38, 76) differ (string compare on first 38)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (197, 386) differ >
  Component "pmid": Numeric: lengths (197, 386) differ
  Component "author_pos": Numeric: lengths (197, 386) differ
  Component "last_name": Lengths (197, 386) differ (string compare on first 197)
  Component "fore_name": Lengths (197, 386) differ (string compare on first 197)
  Component "initials": Lengths (197, 386) differ (string compare on first 197)
  Component "suffix": Lengths (197, 386) differ (string compare on first 197)
  Component "valid": Lengths (197, 386) differ (string compare on first 197)
  Component "equal_contrib": Lengths (197, 386) differ (string compare on first 197)
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (218, 453) differ >
  Component "pmid": Numeric: lengths (218, 453) differ
  Component "author_pos": Numeric: lengths (218, 453) differ
  Component "affiliation_pos": Numeric: lengths (218, 453) differ
  Component "affiliation": Lengths (218, 453) differ (string compare on first 218)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author_identifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (18, 60) differ >
  Component "pmid": Numeric: lengths (18, 60) differ
  Component "author_pos": Numeric: lengths (18, 60) differ
  Component "source": Lengths (18, 60) differ (string compare on first 18)
  Component "identifier": Lengths (18, 60) differ (string compare on first 18)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  author_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
  Component "pmid": Numeric: lengths (28, 58) differ
  Component "complete": Lengths (28, 58) differ (string compare on first 28)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  chemical not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (0, 44) differ >
  Component "pmid": Numeric: lengths (0, 44) differ
  Component "registry_number": Lengths (0, 44) differ (string compare on first 0)
  Component "substance_name": Lengths (0, 44) differ (string compare on first 0)
  Component "substance_ui": Lengths (0, 44) differ (string compare on first 0)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  comment not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (3, 8) differ >
  Component "pmid": Numeric: lengths (3, 8) differ
  Component "ref_type": Lengths (3, 8) differ (string compare on first 3)
  Component "ref_pmid": Numeric: lengths (3, 8) differ
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  data_bank not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (4, 6) differ >
  Component "pmid": Numeric: lengths (4, 6) differ
  Component "data_bank_name": Lengths (4, 6) differ (string compare on first 4)
  Component "accession_number": Lengths (4, 6) differ (string compare on first 4)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  grant_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (16, 34) differ >
  Component "pmid": Numeric: lengths (16, 34) differ
  Component "grant_id": Lengths (16, 34) differ (string compare on first 16)
  Component "acronym": Lengths (16, 34) differ (string compare on first 16)
  Component "agency": Lengths (16, 34) differ (string compare on first 16)
  Component "country": Lengths (16, 34) differ (string compare on first 16)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  grant_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (6, 12) differ >
  Component "pmid": Numeric: lengths (6, 12) differ
  Component "complete": Lengths (6, 12) differ (string compare on first 6)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  investigator not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (27, 54) differ >
  Component "pmid": Numeric: lengths (27, 54) differ
  Component "investigator_pos": Numeric: lengths (27, 54) differ
  Component "last_name": Lengths (27, 54) differ (string compare on first 27)
  Component "fore_name": Lengths (27, 54) differ (string compare on first 27)
  Component "initials": Lengths (27, 54) differ (string compare on first 27)
  Component "suffix": Lengths (27, 54) differ (string compare on first 27)
  Component "valid": Lengths (27, 54) differ (string compare on first 27)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  journal not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
  Component "pmid": Numeric: lengths (28, 58) differ
  Component "journal_name": Lengths (28, 58) differ (string compare on first 28)
  Component "journal_iso": Lengths (28, 58) differ (string compare on first 28)
  Component "pub_date": Numeric: lengths (28, 58) differ
  Component "pub_year": Lengths (28, 58) differ (string compare on first 28)
  Component "pub_month": Lengths (28, 58) differ (string compare on first 28)
  Component "pub_day": Lengths (28, 58) differ (string compare on first 28)
  Component "medline_date": Lengths (28, 58) differ (string compare on first 28)
  ...
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  keyword_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (102, 195) differ >
  Component "pmid": Numeric: lengths (102, 195) differ
  Component "keyword_name": Lengths (102, 195) differ (string compare on first 102)
  Component "major_topic": Lengths (102, 195) differ (string compare on first 102)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  keyword_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (20, 39) differ >
  Component "pmid": Numeric: lengths (20, 39) differ
  Component "list_owner": Lengths (20, 39) differ (string compare on first 20)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (0, 256) differ >
  Component "pmid": Numeric: lengths (0, 256) differ
  Component "descriptor_pos": Lengths (0, 256) differ (string compare on first 0)
  Component "descriptor_name": Lengths (0, 256) differ (string compare on first 0)
  Component "descriptor_ui": Lengths (0, 256) differ (string compare on first 0)
  Component "descriptor_major_topic": Lengths (0, 256) differ (string compare on first 0)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  mesh_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (0, 13) differ >
  Component "pmid": Numeric: lengths (0, 13) differ
  Component "indexing_method": Lengths (0, 13) differ (string compare on first 0)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (0, 152) differ >
  Component "pmid": Numeric: lengths (0, 152) differ
  Component "descriptor_pos": Lengths (0, 152) differ (string compare on first 0)
  Component "qualifier_name": Lengths (0, 152) differ (string compare on first 0)
  Component "qualifier_ui": Lengths (0, 152) differ (string compare on first 0)
  Component "qualifier_major_topic": Lengths (0, 152) differ (string compare on first 0)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  other_abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (2, 4) differ >
  Component "pmid": Numeric: lengths (2, 4) differ
  Component "text": Lengths (2, 4) differ (string compare on first 2)
  Component "type": Lengths (2, 4) differ (string compare on first 2)
  Component "language": Lengths (2, 4) differ (string compare on first 2)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  pmid_status not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (28, 106) differ >
  Component "pmid": Numeric: lengths (28, 106) differ
  Component "version": Numeric: lengths (28, 106) differ
  Component "xml_filename": Lengths (28, 106) differ (string compare on first 28)
  Component "status": Lengths (28, 106) differ (string compare on first 28)
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  pub_history not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (127, 254) differ >
  Component "pmid": Numeric: lengths (127, 254) differ
  Component "pub_status": Lengths (127, 254) differ (string compare on first 127)
  Component "pub_date": Numeric: lengths (127, 254) differ
  -- Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard --
  pub_type not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (30, 79) differ >
  Component "pmid": Numeric: lengths (30, 79) differ
  Component "type_name": Lengths (30, 79) differ (string compare on first 30)
  Component "type_id": Lengths (30, 79) differ (string compare on first 30)
  
  [ FAIL 26 | WARN 4 | SKIP 4 | PASS 103 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted