Running ‘testthat.R’ [43m/52m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmparser)
  > 
  > test_check('pmparser')
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
  Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
  ==================================================
  downloaded 21.0 MB
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
  Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
  ==================================================
  downloaded 83.4 MB
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
  Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
  ==================================================
  downloaded 21.0 MB
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
  Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
  ==================================================
  downloaded 83.4 MB
  
  [ FAIL 55 | WARN 0 | SKIP 4 | PASS 132 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3',
    'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique ──
  data_bank not equal to 0L.
  1/1 mismatches
  [1] 424 - 0 == 424
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (18674, 67) differ >
  Component "pmid": Numeric: lengths (18674, 67) differ
  Component "text": Lengths (18674, 67) differ (string compare on first 67)
  Component "text": 67 string mismatches
  Component "label": Lengths (18674, 67) differ (string compare on first 67)
  Component "label": 'is.NA' value mismatch: 16 in current 36 in target
  Component "nlm_category": Lengths (18674, 67) differ (string compare on first 67)
  Component "nlm_category": 'is.NA' value mismatch: 24 in current 36 in target
  Component "abstract_pos": Numeric: lengths (18674, 67) differ
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (2825, 19) differ >
  Component "pmid": Numeric: lengths (2825, 19) differ
  Component "copyright": Lengths (2825, 19) differ (string compare on first 19)
  Component "copyright": 19 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  article not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
  Component "pmid": Numeric: lengths (11553, 30) differ
  Component "title": Lengths (11553, 30) differ (string compare on first 30)
  Component "title": 30 string mismatches
  Component "language": Lengths (11553, 30) differ (string compare on first 30)
  Component "language": 1 string mismatch
  Component "vernacular_title": Lengths (11553, 30) differ (string compare on first 30)
  Component "vernacular_title": 'is.NA' value mismatch: 29 in current 30 in target
  Component "pub_model": Lengths (11553, 30) differ (string compare on first 30)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  article_id not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (11582, 47) differ >
  Component "pmid": Numeric: lengths (11582, 47) differ
  Component "id_type": Lengths (11582, 47) differ (string compare on first 47)
  Component "id_type": 32 string mismatches
  Component "id_value": Lengths (11582, 47) differ (string compare on first 47)
  Component "id_value": 47 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  author not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (76148, 198) differ >
  Component "pmid": Numeric: lengths (76148, 198) differ
  Component "author_pos": Numeric: lengths (76148, 198) differ
  Component "last_name": Lengths (76148, 198) differ (string compare on first 198)
  Component "last_name": 'is.NA' value mismatch: 2 in current 0 in target
  Component "fore_name": Lengths (76148, 198) differ (string compare on first 198)
  Component "fore_name": 'is.NA' value mismatch: 2 in current 0 in target
  Component "initials": Lengths (76148, 198) differ (string compare on first 198)
  Component "initials": 'is.NA' value mismatch: 2 in current 0 in target
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (93126, 236) differ >
  Component "pmid": Numeric: lengths (93126, 236) differ
  Component "author_pos": Numeric: lengths (93126, 236) differ
  Component "affiliation_pos": Numeric: lengths (93126, 236) differ
  Component "affiliation": Lengths (93126, 236) differ (string compare on first 236)
  Component "affiliation": 236 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (522, 0) differ >
  Component "pmid": Numeric: lengths (522, 0) differ
  Component "author_pos": Numeric: lengths (522, 0) differ
  Component "affiliation_pos": Numeric: lengths (522, 0) differ
  Component "source": Lengths (522, 0) differ (string compare on first 0)
  Component "identifier": Lengths (522, 0) differ (string compare on first 0)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  author_identifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (28358, 52) differ >
  Component "pmid": Numeric: lengths (28358, 52) differ
  Component "author_pos": Numeric: lengths (28358, 52) differ
  Component "source": Lengths (28358, 52) differ (string compare on first 52)
  Component "identifier": Lengths (28358, 52) differ (string compare on first 52)
  Component "identifier": 52 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  author_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (11479, 29) differ >
  Component "pmid": Numeric: lengths (11479, 29) differ
  Component "complete": Lengths (11479, 29) differ (string compare on first 29)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  chemical not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (6509, 9) differ >
  Component "pmid": Numeric: lengths (6509, 9) differ
  Component "registry_number": Lengths (6509, 9) differ (string compare on first 9)
  Component "registry_number": 7 string mismatches
  Component "substance_name": Lengths (6509, 9) differ (string compare on first 9)
  Component "substance_name": 9 string mismatches
  Component "substance_ui": Lengths (6509, 9) differ (string compare on first 9)
  Component "substance_ui": 9 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  comment not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (168, 2) differ >
  Component "pmid": Numeric: lengths (168, 2) differ
  Component "ref_type": Lengths (168, 2) differ (string compare on first 2)
  Component "ref_type": 2 string mismatches
  Component "ref_pmid": Numeric: lengths (168, 2) differ
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  data_bank not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (97, 3) differ >
  Component "pmid": Numeric: lengths (97, 3) differ
  Component "data_bank_name": Lengths (97, 3) differ (string compare on first 3)
  Component "data_bank_name": 1 string mismatch
  Component "accession_number": Lengths (97, 3) differ (string compare on first 3)
  Component "accession_number": 3 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  grant_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (9304, 16) differ >
  Component "pmid": Numeric: lengths (9304, 16) differ
  Component "grant_id": Lengths (9304, 16) differ (string compare on first 16)
  Component "grant_id": 'is.NA' value mismatch: 2 in current 5 in target
  Component "acronym": Lengths (9304, 16) differ (string compare on first 16)
  Component "acronym": 'is.NA' value mismatch: 13 in current 15 in target
  Component "agency": Lengths (9304, 16) differ (string compare on first 16)
  Component "agency": 16 string mismatches
  Component "country": Lengths (9304, 16) differ (string compare on first 16)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  grant_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (4600, 6) differ >
  Component "pmid": Numeric: lengths (4600, 6) differ
  Component "complete": Lengths (4600, 6) differ (string compare on first 6)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  investigator not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (2250, 73) differ >
  Component "pmid": Numeric: lengths (2250, 73) differ
  Component "investigator_pos": Numeric: lengths (2250, 73) differ
  Component "last_name": Lengths (2250, 73) differ (string compare on first 73)
  Component "last_name": 73 string mismatches
  Component "fore_name": Lengths (2250, 73) differ (string compare on first 73)
  Component "fore_name": 73 string mismatches
  Component "initials": Lengths (2250, 73) differ (string compare on first 73)
  Component "initials": 72 string mismatches
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (662, 0) differ >
  Component "pmid": Numeric: lengths (662, 0) differ
  Component "investigator_pos": Numeric: lengths (662, 0) differ
  Component "affiliation_pos": Numeric: lengths (662, 0) differ
  Component "affiliation": Lengths (662, 0) differ (string compare on first 0)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  journal not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
  Component "pmid": Numeric: lengths (11553, 30) differ
  Component "journal_name": Lengths (11553, 30) differ (string compare on first 30)
  Component "journal_name": 30 string mismatches
  Component "journal_iso": Lengths (11553, 30) differ (string compare on first 30)
  Component "journal_iso": 30 string mismatches
  Component "pub_date": Numeric: lengths (11553, 30) differ
  Component "pub_year": Lengths (11553, 30) differ (string compare on first 30)
  Component "pub_year": 30 string mismatches
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  keyword_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (51070, 96) differ >
  Component "pmid": Numeric: lengths (51070, 96) differ
  Component "keyword_name": Lengths (51070, 96) differ (string compare on first 96)
  Component "keyword_name": 96 string mismatches
  Component "major_topic": Lengths (51070, 96) differ (string compare on first 96)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  keyword_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (9382, 20) differ >
  Component "pmid": Numeric: lengths (9382, 20) differ
  Component "list_owner": Lengths (9382, 20) differ (string compare on first 20)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (37767, 42) differ >
  Component "pmid": Numeric: lengths (37767, 42) differ
  Component "descriptor_pos": Lengths (37767, 42) differ (string compare on first 42)
  Component "descriptor_pos": 34 string mismatches
  Component "descriptor_name": Lengths (37767, 42) differ (string compare on first 42)
  Component "descriptor_name": 42 string mismatches
  Component "descriptor_ui": Lengths (37767, 42) differ (string compare on first 42)
  Component "descriptor_ui": 42 string mismatches
  Component "descriptor_major_topic": Lengths (37767, 42) differ (string compare on first 42)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  mesh_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
  Component "pmid": Numeric: lengths (11553, 30) differ
  Component "indexing_method": Lengths (11553, 30) differ (string compare on first 30)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (24517, 14) differ >
  Component "pmid": Numeric: lengths (24517, 14) differ
  Component "descriptor_pos": Lengths (24517, 14) differ (string compare on first 14)
  Component "descriptor_pos": 13 string mismatches
  Component "qualifier_name": Lengths (24517, 14) differ (string compare on first 14)
  Component "qualifier_name": 13 string mismatches
  Component "qualifier_ui": Lengths (24517, 14) differ (string compare on first 14)
  Component "qualifier_ui": 13 string mismatches
  Component "qualifier_major_topic": Lengths (24517, 14) differ (string compare on first 14)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  other_abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (144, 2) differ >
  Component "pmid": Numeric: lengths (144, 2) differ
  Component "text": Lengths (144, 2) differ (string compare on first 2)
  Component "text": 2 string mismatches
  Component "type": Lengths (144, 2) differ (string compare on first 2)
  Component "type": 1 string mismatch
  Component "language": Lengths (144, 2) differ (string compare on first 2)
  Component "language": 1 string mismatch
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  pmid_status not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
  Component "pmid": Numeric: lengths (11553, 30) differ
  Component "version": Numeric: lengths (11553, 30) differ
  Component "xml_filename": Lengths (11553, 30) differ (string compare on first 30)
  Component "xml_filename": 30 string mismatches
  Component "status": Lengths (11553, 30) differ (string compare on first 30)
  Component "status": 19 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  pub_history not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (61521, 149) differ >
  Component "pmid": Numeric: lengths (61521, 149) differ
  Component "pub_status": Lengths (61521, 149) differ (string compare on first 149)
  Component "pub_status": 110 string mismatches
  Component "pub_date": Numeric: lengths (61521, 149) differ
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  pub_type not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (14141, 36) differ >
  Component "pmid": Numeric: lengths (14141, 36) differ
  Component "type_name": Lengths (14141, 36) differ (string compare on first 36)
  Component "type_name": 13 string mismatches
  Component "type_id": Lengths (14141, 36) differ (string compare on first 36)
  Component "type_id": 13 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  readme not equal to DBI::dbReadTable(conExp, tableName).
  Component "text": 1 string mismatch
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (57079, 89) differ >
  Component "pmid": Numeric: lengths (57079, 89) differ
  Component "text": Lengths (57079, 89) differ (string compare on first 89)
  Component "text": 22 string mismatches
  Component "label": Lengths (57079, 89) differ (string compare on first 89)
  Component "label": 'is.NA' value mismatch: 38 in current 18 in target
  Component "nlm_category": Lengths (57079, 89) differ (string compare on first 89)
  Component "nlm_category": 'is.NA' value mismatch: 46 in current 26 in target
  Component "abstract_pos": Numeric: lengths (57079, 89) differ
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (15930, 21) differ >
  Component "pmid": Numeric: lengths (15930, 21) differ
  Component "copyright": Lengths (15930, 21) differ (string compare on first 21)
  Component "copyright": 2 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  article not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (30027, 60) differ >
  Component "pmid": Numeric: lengths (30027, 60) differ
  Component "title": Lengths (30027, 60) differ (string compare on first 60)
  Component "title": 32 string mismatches
  Component "language": Lengths (30027, 60) differ (string compare on first 60)
  Component "language": 3 string mismatches
  Component "vernacular_title": Lengths (30027, 60) differ (string compare on first 60)
  Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target
  Component "pub_model": Lengths (30027, 60) differ (string compare on first 60)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  article_id not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (43707, 78) differ >
  Component "pmid": Numeric: lengths (43707, 78) differ
  Component "id_type": Lengths (43707, 78) differ (string compare on first 78)
  Component "id_type": 12 string mismatches
  Component "id_value": Lengths (43707, 78) differ (string compare on first 78)
  Component "id_value": 33 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  author not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (213197, 337) differ >
  Component "pmid": Numeric: lengths (213197, 337) differ
  Component "author_pos": Numeric: lengths (213197, 337) differ
  Component "last_name": Lengths (213197, 337) differ (string compare on first 337)
  Component "last_name": 153 string mismatches
  Component "fore_name": Lengths (213197, 337) differ (string compare on first 337)
  Component "fore_name": 'is.NA' value mismatch: 2 in current 4 in target
  Component "initials": Lengths (213197, 337) differ (string compare on first 337)
  Component "initials": 'is.NA' value mismatch: 2 in current 4 in target
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (253417, 260) differ >
  Component "pmid": Numeric: lengths (253417, 260) differ
  Component "author_pos": Numeric: lengths (253417, 260) differ
  Component "affiliation_pos": Numeric: lengths (253417, 260) differ
  Component "affiliation": Lengths (253417, 260) differ (string compare on first 260)
  Component "affiliation": 49 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (2130, 0) differ >
  Component "pmid": Numeric: lengths (2130, 0) differ
  Component "author_pos": Numeric: lengths (2130, 0) differ
  Component "affiliation_pos": Numeric: lengths (2130, 0) differ
  Component "source": Lengths (2130, 0) differ (string compare on first 0)
  Component "identifier": Lengths (2130, 0) differ (string compare on first 0)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  author_identifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (56970, 52) differ >
  Component "pmid": Numeric: lengths (56970, 52) differ
  Component "author_pos": Numeric: lengths (56970, 52) differ
  Component "source": Lengths (56970, 52) differ (string compare on first 52)
  Component "identifier": Lengths (56970, 52) differ (string compare on first 52)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  author_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (29746, 59) differ >
  Component "pmid": Numeric: lengths (29746, 59) differ
  Component "complete": Lengths (29746, 59) differ (string compare on first 59)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  chemical not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (24642, 162) differ >
  Component "pmid": Numeric: lengths (24642, 162) differ
  Component "registry_number": Lengths (24642, 162) differ (string compare on first 162)
  Component "registry_number": 83 string mismatches
  Component "substance_name": Lengths (24642, 162) differ (string compare on first 162)
  Component "substance_name": 153 string mismatches
  Component "substance_ui": Lengths (24642, 162) differ (string compare on first 162)
  Component "substance_ui": 153 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  comment not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (1415, 6) differ >
  Component "pmid": Numeric: lengths (1415, 6) differ
  Component "ref_type": Lengths (1415, 6) differ (string compare on first 6)
  Component "ref_type": 2 string mismatches
  Component "ref_pmid": Numeric: lengths (1415, 6) differ
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  data_bank not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (956, 9) differ >
  Component "pmid": Numeric: lengths (956, 9) differ
  Component "data_bank_name": Lengths (956, 9) differ (string compare on first 9)
  Component "data_bank_name": 5 string mismatches
  Component "accession_number": Lengths (956, 9) differ (string compare on first 9)
  Component "accession_number": 6 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  grant_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (30455, 43) differ >
  Component "pmid": Numeric: lengths (30455, 43) differ
  Component "grant_id": Lengths (30455, 43) differ (string compare on first 43)
  Component "grant_id": 27 string mismatches
  Component "acronym": Lengths (30455, 43) differ (string compare on first 43)
  Component "acronym": 'is.NA' value mismatch: 13 in current 14 in target
  Component "agency": Lengths (30455, 43) differ (string compare on first 43)
  Component "agency": 24 string mismatches
  Component "country": Lengths (30455, 43) differ (string compare on first 43)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  grant_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (10488, 16) differ >
  Component "pmid": Numeric: lengths (10488, 16) differ
  Component "complete": Lengths (10488, 16) differ (string compare on first 16)
  Component "complete": 1 string mismatch
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  investigator not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (18563, 76) differ >
  Component "pmid": Numeric: lengths (18563, 76) differ
  Component "investigator_pos": Numeric: lengths (18563, 76) differ
  Component "last_name": Lengths (18563, 76) differ (string compare on first 76)
  Component "last_name": 3 string mismatches
  Component "fore_name": Lengths (18563, 76) differ (string compare on first 76)
  Component "fore_name": 3 string mismatches
  Component "initials": Lengths (18563, 76) differ (string compare on first 76)
  Component "initials": 3 string mismatches
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (1552, 3) differ >
  Component "pmid": Numeric: lengths (1552, 3) differ
  Component "investigator_pos": Numeric: lengths (1552, 3) differ
  Component "affiliation_pos": Numeric: lengths (1552, 3) differ
  Component "affiliation": Lengths (1552, 3) differ (string compare on first 3)
  Component "affiliation": 3 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  journal not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (30027, 60) differ >
  Component "pmid": Numeric: lengths (30027, 60) differ
  Component "journal_name": Lengths (30027, 60) differ (string compare on first 60)
  Component "journal_name": 32 string mismatches
  Component "journal_iso": Lengths (30027, 60) differ (string compare on first 60)
  Component "journal_iso": 32 string mismatches
  Component "pub_date": Numeric: lengths (30027, 60) differ
  Component "pub_year": Lengths (30027, 60) differ (string compare on first 60)
  Component "pub_year": 30 string mismatches
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  keyword_item not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (113134, 128) differ >
  Component "pmid": Numeric: lengths (113134, 128) differ
  Component "keyword_name": Lengths (113134, 128) differ (string compare on first 128)
  Component "keyword_name": 32 string mismatches
  Component "major_topic": Lengths (113134, 128) differ (string compare on first 128)
  Component "major_topic": 22 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  keyword_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (21490, 27) differ >
  Component "pmid": Numeric: lengths (21490, 27) differ
  Component "list_owner": Lengths (21490, 27) differ (string compare on first 27)
  Component "list_owner": 7 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (165001, 469) differ >
  Component "pmid": Numeric: lengths (165001, 469) differ
  Component "descriptor_pos": Lengths (165001, 469) differ (string compare on first 469)
  Component "descriptor_pos": 420 string mismatches
  Component "descriptor_name": Lengths (165001, 469) differ (string compare on first 469)
  Component "descriptor_name": 425 string mismatches
  Component "descriptor_ui": Lengths (165001, 469) differ (string compare on first 469)
  Component "descriptor_ui": 425 string mismatches
  Component "descriptor_major_topic": Lengths (165001, 469) differ (string compare on first 469)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  mesh_list not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (15126, 34) differ >
  Component "pmid": Numeric: lengths (15126, 34) differ
  Component "indexing_method": Lengths (15126, 34) differ (string compare on first 34)
  Component "indexing_method": 5 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (101110, 352) differ >
  Component "pmid": Numeric: lengths (101110, 352) differ
  Component "descriptor_pos": Lengths (101110, 352) differ (string compare on first 352)
  Component "descriptor_pos": 318 string mismatches
  Component "qualifier_name": Lengths (101110, 352) differ (string compare on first 352)
  Component "qualifier_name": 325 string mismatches
  Component "qualifier_ui": Lengths (101110, 352) differ (string compare on first 352)
  Component "qualifier_ui": 325 string mismatches
  Component "qualifier_major_topic": Lengths (101110, 352) differ (string compare on first 352)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  other_abstract not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (393, 4) differ >
  Component "pmid": Numeric: lengths (393, 4) differ
  Component "text": Lengths (393, 4) differ (string compare on first 4)
  Component "text": 3 string mismatches
  Component "type": Lengths (393, 4) differ (string compare on first 4)
  Component "type": 3 string mismatches
  Component "language": Lengths (393, 4) differ (string compare on first 4)
  Component "language": 2 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  other_id not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (3, 6) differ >
  Component "pmid": Numeric: lengths (3, 6) differ
  Component "source": Lengths (3, 6) differ (string compare on first 3)
  Component "source": 3 string mismatches
  Component "id_value": Lengths (3, 6) differ (string compare on first 3)
  Component "id_value": 3 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  pmid_status not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (34007, 60) differ >
  Component "pmid": Numeric: lengths (34007, 60) differ
  Component "version": Numeric: lengths (34007, 60) differ
  Component "xml_filename": Lengths (34007, 60) differ (string compare on first 60)
  Component "xml_filename": 31 string mismatches
  Component "status": Lengths (34007, 60) differ (string compare on first 60)
  Component "status": 2 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  pub_history not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (147532, 250) differ >
  Component "pmid": Numeric: lengths (147532, 250) differ
  Component "pub_status": Lengths (147532, 250) differ (string compare on first 250)
  Component "pub_status": 49 string mismatches
  Component "pub_date": Numeric: lengths (147532, 250) differ
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  pub_type not equal to DBI::dbReadTable(conExp, tableName).
  Attributes: < Component "row.names": Numeric: lengths (40895, 105) differ >
  Component "pmid": Numeric: lengths (40895, 105) differ
  Component "type_name": Lengths (40895, 105) differ (string compare on first 105)
  Component "type_name": 54 string mismatches
  Component "type_id": Lengths (40895, 105) differ (string compare on first 105)
  Component "type_id": 54 string mismatches
  
  [ FAIL 55 | WARN 0 | SKIP 4 | PASS 132 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted