Running 'testthat.R' [14m]
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/pubmed26n1334.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz'
  Content type 'application/x-gzip' length 13837691 bytes (13.2 MB)
  ==================================================
  downloaded 13.2 MB
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz'
  Content type 'application/x-gzip' length 44629574 bytes (42.6 MB)
  ==================================================
  downloaded 42.6 MB
  
  Saving _problems/test_modify_pubmed_db_dup-76.R
  Saving _problems/test_modify_pubmed_db_dup-76.R
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz'
  Content type 'application/x-gzip' length 13837691 bytes (13.2 MB)
  ==================================================
  downloaded 13.2 MB
  
  Saving _problems/test_modify_pubmed_db_std-34.R
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  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz'
  Content type 'application/x-gzip' length 44629574 bytes (42.6 MB)
  ==================================================
  downloaded 42.6 MB
  
  Saving _problems/test_modify_pubmed_db_std-54.R
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  Saving _problems/test_modify_pubmed_db_std-54.R
  [ FAIL 56 | WARN 4 | SKIP 4 | PASS 131 ]
  
  ══ 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 ──
  Expected data_bank to equal 0L.
  Differences:
  1/1 mismatches
  [1] 101 - 0 == 101
  ── Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique ──
  Expected mesh_qualifier to equal 0L.
  Differences:
  1/1 mismatches
  [1] 405 - 0 == 405
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected abstract to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (9603, 68) differ >
  Component "pmid": Numeric: lengths (9603, 68) differ
  Component "text": Lengths (9603, 68) differ (string compare on first 68)
  Component "text": 68 string mismatches
  Component "label": Lengths (9603, 68) differ (string compare on first 68)
  Component "label": 'is.NA' value mismatch: 15 in current 13 in target
  Component "nlm_category": Lengths (9603, 68) differ (string compare on first 68)
  Component "nlm_category": 'is.NA' value mismatch: 15 in current 13 in target
  Component "abstract_pos": Numeric: lengths (9603, 68) differ
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected abstract_copyright to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (3219, 22) differ >
  Component "pmid": Numeric: lengths (3219, 22) differ
  Component "copyright": Lengths (3219, 22) differ (string compare on first 22)
  Component "copyright": 22 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected article to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >
  Component "pmid": Numeric: lengths (4989, 30) differ
  Component "title": Lengths (4989, 30) differ (string compare on first 30)
  Component "title": 30 string mismatches
  Component "language": Lengths (4989, 30) differ (string compare on first 30)
  Component "language": 2 string mismatches
  Component "vernacular_title": Lengths (4989, 30) differ (string compare on first 30)
  Component "vernacular_title": 'is.NA' value mismatch: 28 in current 30 in target
  Component "pub_model": Lengths (4989, 30) differ (string compare on first 30)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected article_id to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (6359, 40) differ >
  Component "pmid": Numeric: lengths (6359, 40) differ
  Component "id_type": Lengths (6359, 40) differ (string compare on first 40)
  Component "id_type": 10 string mismatches
  Component "id_value": Lengths (6359, 40) differ (string compare on first 40)
  Component "id_value": 40 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected author to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (34978, 279) differ >
  Component "pmid": Numeric: lengths (34978, 279) differ
  Component "author_pos": Numeric: lengths (34978, 279) differ
  Component "last_name": Lengths (34978, 279) differ (string compare on first 279)
  Component "last_name": 'is.NA' value mismatch: 4 in current 0 in target
  Component "fore_name": Lengths (34978, 279) differ (string compare on first 279)
  Component "fore_name": 'is.NA' value mismatch: 5 in current 0 in target
  Component "initials": Lengths (34978, 279) differ (string compare on first 279)
  Component "initials": 'is.NA' value mismatch: 5 in current 0 in target
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected author_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (42448, 337) differ >
  Component "pmid": Numeric: lengths (42448, 337) differ
  Component "author_pos": Numeric: lengths (42448, 337) differ
  Component "affiliation_pos": Numeric: lengths (42448, 337) differ
  Component "affiliation": Lengths (42448, 337) differ (string compare on first 337)
  Component "affiliation": 337 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected author_affiliation_identifier to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (989, 0) differ >
  Component "pmid": Numeric: lengths (989, 0) differ
  Component "author_pos": Numeric: lengths (989, 0) differ
  Component "affiliation_pos": Numeric: lengths (989, 0) differ
  Component "source": Lengths (989, 0) differ (string compare on first 0)
  Component "identifier": Lengths (989, 0) differ (string compare on first 0)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected author_identifier to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (7607, 29) differ >
  Component "pmid": Numeric: lengths (7607, 29) differ
  Component "author_pos": Numeric: lengths (7607, 29) differ
  Component "source": Lengths (7607, 29) differ (string compare on first 29)
  Component "identifier": Lengths (7607, 29) differ (string compare on first 29)
  Component "identifier": 29 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected author_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (4932, 30) differ >
  Component "pmid": Numeric: lengths (4932, 30) differ
  Component "complete": Lengths (4932, 30) differ (string compare on first 30)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected chemical to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (1777, 5) differ >
  Component "pmid": Numeric: lengths (1777, 5) differ
  Component "registry_number": Lengths (1777, 5) differ (string compare on first 5)
  Component "registry_number": 3 string mismatches
  Component "substance_name": Lengths (1777, 5) differ (string compare on first 5)
  Component "substance_name": 5 string mismatches
  Component "substance_ui": Lengths (1777, 5) differ (string compare on first 5)
  Component "substance_ui": 5 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected comment to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (150, 3) differ >
  Component "pmid": Numeric: lengths (150, 3) differ
  Component "ref_type": Lengths (150, 3) differ (string compare on first 3)
  Component "ref_type": 1 string mismatch
  Component "ref_pmid": Numeric: lengths (150, 3) differ
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected data_bank to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (70, 4) differ >
  Component "pmid": Numeric: lengths (70, 4) differ
  Component "data_bank_name": Lengths (70, 4) differ (string compare on first 4)
  Component "accession_number": Lengths (70, 4) differ (string compare on first 4)
  Component "accession_number": 4 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected grant_item to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (2637, 35) differ >
  Component "pmid": Numeric: lengths (2637, 35) differ
  Component "grant_id": Lengths (2637, 35) differ (string compare on first 35)
  Component "grant_id": 'is.NA' value mismatch: 6 in current 8 in target
  Component "acronym": Lengths (2637, 35) differ (string compare on first 35)
  Component "acronym": 'is.NA' value mismatch: 20 in current 34 in target
  Component "agency": Lengths (2637, 35) differ (string compare on first 35)
  Component "agency": 35 string mismatches
  Component "country": Lengths (2637, 35) differ (string compare on first 35)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected grant_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (909, 8) differ >
  Component "pmid": Numeric: lengths (909, 8) differ
  Component "complete": Lengths (909, 8) differ (string compare on first 8)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected investigator to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (2074, 80) differ >
  Component "pmid": Numeric: lengths (2074, 80) differ
  Component "investigator_pos": Numeric: lengths (2074, 80) differ
  Component "last_name": Lengths (2074, 80) differ (string compare on first 80)
  Component "last_name": 80 string mismatches
  Component "fore_name": Lengths (2074, 80) differ (string compare on first 80)
  Component "fore_name": 80 string mismatches
  Component "initials": Lengths (2074, 80) differ (string compare on first 80)
  Component "initials": 73 string mismatches
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected investigator_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (45, 53) differ >
  Component "pmid": Numeric: lengths (45, 53) differ
  Component "investigator_pos": Numeric: lengths (45, 53) differ
  Component "affiliation_pos": Numeric: lengths (45, 53) differ
  Component "affiliation": Lengths (45, 53) differ (string compare on first 45)
  Component "affiliation": 45 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected journal to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >
  Component "pmid": Numeric: lengths (4989, 30) differ
  Component "journal_name": Lengths (4989, 30) differ (string compare on first 30)
  Component "journal_name": 30 string mismatches
  Component "journal_iso": Lengths (4989, 30) differ (string compare on first 30)
  Component "journal_iso": 30 string mismatches
  Component "pub_date": Numeric: lengths (4989, 30) differ
  Component "pub_year": Lengths (4989, 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 ──
  Expected keyword_item to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (19167, 109) differ >
  Component "pmid": Numeric: lengths (19167, 109) differ
  Component "keyword_name": Lengths (19167, 109) differ (string compare on first 109)
  Component "keyword_name": 109 string mismatches
  Component "major_topic": Lengths (19167, 109) differ (string compare on first 109)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected keyword_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (3596, 21) differ >
  Component "pmid": Numeric: lengths (3596, 21) differ
  Component "list_owner": Lengths (3596, 21) differ (string compare on first 21)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected mesh_descriptor to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (11460, 74) differ >
  Component "pmid": Numeric: lengths (11460, 74) differ
  Component "descriptor_pos": Lengths (11460, 74) differ (string compare on first 74)
  Component "descriptor_pos": 65 string mismatches
  Component "descriptor_name": Lengths (11460, 74) differ (string compare on first 74)
  Component "descriptor_name": 71 string mismatches
  Component "descriptor_ui": Lengths (11460, 74) differ (string compare on first 74)
  Component "descriptor_ui": 71 string mismatches
  Component "descriptor_major_topic": Lengths (11460, 74) differ (string compare on first 74)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected mesh_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >
  Component "pmid": Numeric: lengths (4989, 30) differ
  Component "indexing_method": Lengths (4989, 30) differ (string compare on first 30)
  Component "indexing_method": 1 string mismatch
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected mesh_qualifier to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (7130, 39) differ >
  Component "pmid": Numeric: lengths (7130, 39) differ
  Component "descriptor_pos": Lengths (7130, 39) differ (string compare on first 39)
  Component "descriptor_pos": 35 string mismatches
  Component "qualifier_name": Lengths (7130, 39) differ (string compare on first 39)
  Component "qualifier_name": 38 string mismatches
  Component "qualifier_ui": Lengths (7130, 39) differ (string compare on first 39)
  Component "qualifier_ui": 38 string mismatches
  Component "qualifier_major_topic": Lengths (7130, 39) differ (string compare on first 39)
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected other_abstract to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (147, 4) differ >
  Component "pmid": Numeric: lengths (147, 4) differ
  Component "text": Lengths (147, 4) differ (string compare on first 4)
  Component "text": 4 string mismatches
  Component "type": Lengths (147, 4) differ (string compare on first 4)
  Component "type": 2 string mismatches
  Component "language": Lengths (147, 4) differ (string compare on first 4)
  Component "language": 4 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected pmid_status to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >
  Component "pmid": Numeric: lengths (4989, 30) differ
  Component "version": Numeric: lengths (4989, 30) differ
  Component "xml_filename": Lengths (4989, 30) differ (string compare on first 30)
  Component "xml_filename": 30 string mismatches
  Component "status": Lengths (4989, 30) differ (string compare on first 30)
  Component "status": 14 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected pub_history to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (22724, 143) differ >
  Component "pmid": Numeric: lengths (22724, 143) differ
  Component "pub_status": Lengths (22724, 143) differ (string compare on first 143)
  Component "pub_status": 100 string mismatches
  Component "pub_date": Numeric: lengths (22724, 143) differ
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected pub_type to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (6060, 37) differ >
  Component "pmid": Numeric: lengths (6060, 37) differ
  Component "type_name": Lengths (6060, 37) differ (string compare on first 37)
  Component "type_name": 12 string mismatches
  Component "type_id": Lengths (6060, 37) differ (string compare on first 37)
  Component "type_id": 12 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected readme to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Component "text": 1 string mismatch
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected abstract to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (27961, 126) differ >
  Component "pmid": Numeric: lengths (27961, 126) differ
  Component "text": Lengths (27961, 126) differ (string compare on first 126)
  Component "text": 58 string mismatches
  Component "label": Lengths (27961, 126) differ (string compare on first 126)
  Component "label": 'is.NA' value mismatch: 34 in current 27 in target
  Component "nlm_category": Lengths (27961, 126) differ (string compare on first 126)
  Component "nlm_category": 'is.NA' value mismatch: 34 in current 50 in target
  Component "abstract_pos": Numeric: lengths (27961, 126) differ
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected abstract_copyright to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (9124, 43) differ >
  Component "pmid": Numeric: lengths (9124, 43) differ
  Component "copyright": Lengths (9124, 43) differ (string compare on first 43)
  Component "copyright": 21 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected article to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ >
  Component "pmid": Numeric: lengths (14308, 60) differ
  Component "title": Lengths (14308, 60) differ (string compare on first 60)
  Component "title": 30 string mismatches
  Component "language": Lengths (14308, 60) differ (string compare on first 60)
  Component "vernacular_title": Lengths (14308, 60) differ (string compare on first 60)
  Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target
  Component "pub_model": Lengths (14308, 60) differ (string compare on first 60)
  Component "pub_model": 19 string mismatches
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected article_id to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (16828, 76) differ >
  Component "pmid": Numeric: lengths (16828, 76) differ
  Component "id_type": Lengths (16828, 76) differ (string compare on first 76)
  Component "id_type": 10 string mismatches
  Component "id_value": Lengths (16828, 76) differ (string compare on first 76)
  Component "id_value": 36 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected author to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (101991, 490) differ >
  Component "pmid": Numeric: lengths (101991, 490) differ
  Component "author_pos": Numeric: lengths (101991, 490) differ
  Component "last_name": Lengths (101991, 490) differ (string compare on first 490)
  Component "last_name": 'is.NA' value mismatch: 6 in current 4 in target
  Component "fore_name": Lengths (101991, 490) differ (string compare on first 490)
  Component "fore_name": 'is.NA' value mismatch: 7 in current 5 in target
  Component "initials": Lengths (101991, 490) differ (string compare on first 490)
  Component "initials": 'is.NA' value mismatch: 7 in current 5 in target
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected author_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (121076, 614) differ >
  Component "pmid": Numeric: lengths (121076, 614) differ
  Component "author_pos": Numeric: lengths (121076, 614) differ
  Component "affiliation_pos": Numeric: lengths (121076, 614) differ
  Component "affiliation": Lengths (121076, 614) differ (string compare on first 614)
  Component "affiliation": 277 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected author_affiliation_identifier to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (3559, 0) differ >
  Component "pmid": Numeric: lengths (3559, 0) differ
  Component "author_pos": Numeric: lengths (3559, 0) differ
  Component "affiliation_pos": Numeric: lengths (3559, 0) differ
  Component "source": Lengths (3559, 0) differ (string compare on first 0)
  Component "identifier": Lengths (3559, 0) differ (string compare on first 0)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected author_identifier to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (21074, 61) differ >
  Component "pmid": Numeric: lengths (21074, 61) differ
  Component "author_pos": Numeric: lengths (21074, 61) differ
  Component "source": Lengths (21074, 61) differ (string compare on first 61)
  Component "identifier": Lengths (21074, 61) differ (string compare on first 61)
  Component "identifier": 32 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected author_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (14209, 59) differ >
  Component "pmid": Numeric: lengths (14209, 59) differ
  Component "complete": Lengths (14209, 59) differ (string compare on first 59)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected chemical to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (9674, 16) differ >
  Component "pmid": Numeric: lengths (9674, 16) differ
  Component "registry_number": Lengths (9674, 16) differ (string compare on first 16)
  Component "registry_number": 8 string mismatches
  Component "substance_name": Lengths (9674, 16) differ (string compare on first 16)
  Component "substance_name": 11 string mismatches
  Component "substance_ui": Lengths (9674, 16) differ (string compare on first 16)
  Component "substance_ui": 11 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected comment to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (898, 6) differ >
  Component "pmid": Numeric: lengths (898, 6) differ
  Component "ref_type": Lengths (898, 6) differ (string compare on first 6)
  Component "ref_type": 3 string mismatches
  Component "ref_pmid": Numeric: lengths (898, 6) differ
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected data_bank to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (267, 6) differ >
  Component "pmid": Numeric: lengths (267, 6) differ
  Component "data_bank_name": Lengths (267, 6) differ (string compare on first 6)
  Component "data_bank_name": 1 string mismatch
  Component "accession_number": Lengths (267, 6) differ (string compare on first 6)
  Component "accession_number": 2 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected grant_item to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (8770, 57) differ >
  Component "pmid": Numeric: lengths (8770, 57) differ
  Component "grant_id": Lengths (8770, 57) differ (string compare on first 57)
  Component "grant_id": 'is.NA' value mismatch: 13 in current 8 in target
  Component "acronym": Lengths (8770, 57) differ (string compare on first 57)
  Component "acronym": 'is.NA' value mismatch: 42 in current 22 in target
  Component "agency": Lengths (8770, 57) differ (string compare on first 57)
  Component "agency": 22 string mismatches
  Component "country": Lengths (8770, 57) differ (string compare on first 57)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected grant_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (3033, 17) differ >
  Component "pmid": Numeric: lengths (3033, 17) differ
  Component "complete": Lengths (3033, 17) differ (string compare on first 17)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected investigator to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (5842, 144) differ >
  Component "pmid": Numeric: lengths (5842, 144) differ
  Component "investigator_pos": Numeric: lengths (5842, 144) differ
  Component "last_name": Lengths (5842, 144) differ (string compare on first 144)
  Component "last_name": 64 string mismatches
  Component "fore_name": Lengths (5842, 144) differ (string compare on first 144)
  Component "fore_name": 64 string mismatches
  Component "initials": Lengths (5842, 144) differ (string compare on first 144)
  Component "initials": 59 string mismatches
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected investigator_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (227, 53) differ >
  Component "pmid": Numeric: lengths (227, 53) differ
  Component "investigator_pos": Numeric: lengths (227, 53) differ
  Component "affiliation_pos": Numeric: lengths (227, 53) differ
  Component "affiliation": Lengths (227, 53) differ (string compare on first 53)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected investigator_identifier to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (2, 0) differ >
  Component "pmid": Numeric: lengths (2, 0) differ
  Component "investigator_pos": Numeric: lengths (2, 0) differ
  Component "source": Lengths (2, 0) differ (string compare on first 0)
  Component "identifier": Lengths (2, 0) differ (string compare on first 0)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected journal to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ >
  Component "pmid": Numeric: lengths (14308, 60) differ
  Component "journal_name": Lengths (14308, 60) differ (string compare on first 60)
  Component "journal_name": 30 string mismatches
  Component "journal_iso": Lengths (14308, 60) differ (string compare on first 60)
  Component "journal_iso": 30 string mismatches
  Component "pub_date": Numeric: lengths (14308, 60) differ
  Component "pub_year": Lengths (14308, 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 ──
  Expected keyword_item to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (57226, 229) differ >
  Component "pmid": Numeric: lengths (57226, 229) differ
  Component "keyword_name": Lengths (57226, 229) differ (string compare on first 229)
  Component "keyword_name": 120 string mismatches
  Component "major_topic": Lengths (57226, 229) differ (string compare on first 229)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected keyword_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (10762, 43) differ >
  Component "pmid": Numeric: lengths (10762, 43) differ
  Component "list_owner": Lengths (10762, 43) differ (string compare on first 43)
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected mesh_descriptor to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (72995, 140) differ >
  Component "pmid": Numeric: lengths (72995, 140) differ
  Component "descriptor_pos": Lengths (72995, 140) differ (string compare on first 140)
  Component "descriptor_pos": 51 string mismatches
  Component "descriptor_name": Lengths (72995, 140) differ (string compare on first 140)
  Component "descriptor_name": 66 string mismatches
  Component "descriptor_ui": Lengths (72995, 140) differ (string compare on first 140)
  Component "descriptor_ui": 66 string mismatches
  Component "descriptor_major_topic": Lengths (72995, 140) differ (string compare on first 140)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected mesh_list to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (6973, 36) differ >
  Component "pmid": Numeric: lengths (6973, 36) differ
  Component "indexing_method": Lengths (6973, 36) differ (string compare on first 36)
  Component "indexing_method": 6 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected mesh_qualifier to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (42278, 88) differ >
  Component "pmid": Numeric: lengths (42278, 88) differ
  Component "descriptor_pos": Lengths (42278, 88) differ (string compare on first 88)
  Component "descriptor_pos": 49 string mismatches
  Component "qualifier_name": Lengths (42278, 88) differ (string compare on first 88)
  Component "qualifier_name": 47 string mismatches
  Component "qualifier_ui": Lengths (42278, 88) differ (string compare on first 88)
  Component "qualifier_ui": 47 string mismatches
  Component "qualifier_major_topic": Lengths (42278, 88) differ (string compare on first 88)
  ...
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected other_abstract to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (417, 7) differ >
  Component "pmid": Numeric: lengths (417, 7) differ
  Component "text": Lengths (417, 7) differ (string compare on first 7)
  Component "text": 3 string mismatches
  Component "type": Lengths (417, 7) differ (string compare on first 7)
  Component "type": 2 string mismatches
  Component "language": Lengths (417, 7) differ (string compare on first 7)
  Component "language": 3 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected pmid_status to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (14327, 60) differ >
  Component "pmid": Numeric: lengths (14327, 60) differ
  Component "version": Numeric: lengths (14327, 60) differ
  Component "xml_filename": Lengths (14327, 60) differ (string compare on first 60)
  Component "xml_filename": 30 string mismatches
  Component "status": Lengths (14327, 60) differ (string compare on first 60)
  Component "status": 24 string mismatches
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected pub_history to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (70114, 293) differ >
  Component "pmid": Numeric: lengths (70114, 293) differ
  Component "pub_status": Lengths (70114, 293) differ (string compare on first 293)
  Component "pub_status": 114 string mismatches
  Component "pub_date": Numeric: lengths (70114, 293) differ
  ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
  Expected pub_type to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (19407, 74) differ >
  Component "pmid": Numeric: lengths (19407, 74) differ
  Component "type_name": Lengths (19407, 74) differ (string compare on first 74)
  Component "type_name": 27 string mismatches
  Component "type_id": Lengths (19407, 74) differ (string compare on first 74)
  Component "type_id": 27 string mismatches
  
  [ FAIL 56 | WARN 4 | SKIP 4 | PASS 131 ]
  Error:
  ! Test failures.
  Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted