Running 'testthat.R' [24m]
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/pubmed24n1219.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed24n1219.xml.gz'
  Content type 'application/x-gzip' length 30686089 bytes (29.3 MB)
  ==================================================
  downloaded 29.3 MB
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed24n1220.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed24n1220.xml.gz'
  Content type 'application/x-gzip' length 32921829 bytes (31.4 MB)
  ==================================================
  downloaded 31.4 MB
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed24n1219.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed24n1219.xml.gz'
  Content type 'application/x-gzip' length 30686089 bytes (29.3 MB)
  ==================================================
  downloaded 29.3 MB
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed24n1220.xml.gz.md5'
  Content type 'application/x-gzip' length 60 bytes
  ==================================================
  downloaded 60 bytes
  
  trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed24n1220.xml.gz'
  Content type 'application/x-gzip' length 32921829 bytes (31.4 MB)
  ==================================================
  downloaded 31.4 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:60:5'): modifyPubmedDb create is unique ──
  keyword_item not equal to 0L.
  1/1 mismatches
  [1] 13695 - 0 == 13695
  ── Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique ──
  comment not equal to 0L.
  1/1 mismatches
  [1] 22 - 0 == 22
  ── 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 (28203, 79) differ >
  Component "pmid": Numeric: lengths (28203, 79) differ
  Component "text": Lengths (28203, 79) differ (string compare on first 79)
  Component "text": 79 string mismatches
  Component "label": Lengths (28203, 79) differ (string compare on first 79)
  Component "label": 'is.NA' value mismatch: 14 in current 26 in target
  Component "nlm_category": Lengths (28203, 79) differ (string compare on first 79)
  Component "nlm_category": 'is.NA' value mismatch: 26 in current 40 in target
  Component "abstract_pos": Numeric: lengths (28203, 79) 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 (9293, 25) differ >
  Component "pmid": Numeric: lengths (9293, 25) differ
  Component "copyright": Lengths (9293, 25) differ (string compare on first 25)
  Component "copyright": 25 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 (15432, 32) differ >
  Component "pmid": Numeric: lengths (15432, 32) differ
  Component "title": Lengths (15432, 32) differ (string compare on first 32)
  Component "title": 32 string mismatches
  Component "language": Lengths (15432, 32) differ (string compare on first 32)
  Component "language": 1 string mismatch
  Component "vernacular_title": Lengths (15432, 32) differ (string compare on first 32)
  Component "vernacular_title": 'is.NA' value mismatch: 30 in current 32 in target
  Component "pub_model": Lengths (15432, 32) differ (string compare on first 32)
  ...
  ── 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 (19208, 44) differ >
  Component "pmid": Numeric: lengths (19208, 44) differ
  Component "id_type": Lengths (19208, 44) differ (string compare on first 44)
  Component "id_type": 12 string mismatches
  Component "id_value": Lengths (19208, 44) differ (string compare on first 44)
  Component "id_value": 44 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 (97386, 233) differ >
  Component "pmid": Numeric: lengths (97386, 233) differ
  Component "author_pos": Numeric: lengths (97386, 233) differ
  Component "last_name": Lengths (97386, 233) differ (string compare on first 233)
  Component "last_name": 'is.NA' value mismatch: 3 in current 0 in target
  Component "fore_name": Lengths (97386, 233) differ (string compare on first 233)
  Component "fore_name": 'is.NA' value mismatch: 3 in current 0 in target
  Component "initials": Lengths (97386, 233) differ (string compare on first 233)
  Component "initials": 'is.NA' value mismatch: 3 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 (104883, 274) differ >
  Component "pmid": Numeric: lengths (104883, 274) differ
  Component "author_pos": Numeric: lengths (104883, 274) differ
  Component "affiliation_pos": Numeric: lengths (104883, 274) differ
  Component "affiliation": Lengths (104883, 274) differ (string compare on first 274)
  Component "affiliation": 274 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 (1802, 0) differ >
  Component "pmid": Numeric: lengths (1802, 0) differ
  Component "author_pos": Numeric: lengths (1802, 0) differ
  Component "affiliation_pos": Numeric: lengths (1802, 0) differ
  Component "source": Lengths (1802, 0) differ (string compare on first 0)
  Component "identifier": Lengths (1802, 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 (17240, 33) differ >
  Component "pmid": Numeric: lengths (17240, 33) differ
  Component "author_pos": Numeric: lengths (17240, 33) differ
  Component "source": Lengths (17240, 33) differ (string compare on first 33)
  Component "identifier": Lengths (17240, 33) differ (string compare on first 33)
  Component "identifier": 33 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 (15276, 30) differ >
  Component "pmid": Numeric: lengths (15276, 30) differ
  Component "complete": Lengths (15276, 30) differ (string compare on first 30)
  ── 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 (0, 17) differ >
  Component "pmid": Numeric: lengths (0, 17) differ
  Component "registry_number": Lengths (0, 17) differ (string compare on first 0)
  Component "substance_name": Lengths (0, 17) differ (string compare on first 0)
  Component "substance_ui": Lengths (0, 17) differ (string compare on first 0)
  ── 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 (582, 2) differ >
  Component "pmid": Numeric: lengths (582, 2) differ
  Component "ref_type": Lengths (582, 2) differ (string compare on first 2)
  Component "ref_type": 1 string mismatch
  Component "ref_pmid": Numeric: lengths (582, 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 (180, 5) differ >
  Component "pmid": Numeric: lengths (180, 5) differ
  Component "data_bank_name": Lengths (180, 5) differ (string compare on first 5)
  Component "data_bank_name": 1 string mismatch
  Component "accession_number": Lengths (180, 5) differ (string compare on first 5)
  Component "accession_number": 5 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 (4688, 3) differ >
  Component "pmid": Numeric: lengths (4688, 3) differ
  Component "grant_id": Lengths (4688, 3) differ (string compare on first 3)
  Component "grant_id": 3 string mismatches
  Component "acronym": Lengths (4688, 3) differ (string compare on first 3)
  Component "agency": Lengths (4688, 3) differ (string compare on first 3)
  Component "agency": 3 string mismatches
  Component "country": Lengths (4688, 3) differ (string compare on first 3)
  ── 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 (1953, 3) differ >
  Component "pmid": Numeric: lengths (1953, 3) differ
  Component "complete": Lengths (1953, 3) differ (string compare on first 3)
  ── 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 (4294, 152) differ >
  Component "pmid": Numeric: lengths (4294, 152) differ
  Component "investigator_pos": Numeric: lengths (4294, 152) differ
  Component "last_name": Lengths (4294, 152) differ (string compare on first 152)
  Component "last_name": 152 string mismatches
  Component "fore_name": Lengths (4294, 152) differ (string compare on first 152)
  Component "fore_name": 152 string mismatches
  Component "initials": Lengths (4294, 152) differ (string compare on first 152)
  Component "initials": 150 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 (1322, 0) differ >
  Component "pmid": Numeric: lengths (1322, 0) differ
  Component "investigator_pos": Numeric: lengths (1322, 0) differ
  Component "affiliation_pos": Numeric: lengths (1322, 0) differ
  Component "affiliation": Lengths (1322, 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 (15432, 32) differ >
  Component "pmid": Numeric: lengths (15432, 32) differ
  Component "journal_name": Lengths (15432, 32) differ (string compare on first 32)
  Component "journal_name": 32 string mismatches
  Component "journal_iso": Lengths (15432, 32) differ (string compare on first 32)
  Component "journal_iso": 32 string mismatches
  Component "pub_date": Numeric: lengths (15432, 32) differ
  Component "pub_year": Lengths (15432, 32) differ (string compare on first 32)
  Component "pub_year": 32 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 (45688, 111) differ >
  Component "pmid": Numeric: lengths (45688, 111) differ
  Component "keyword_name": Lengths (45688, 111) differ (string compare on first 111)
  Component "keyword_name": 111 string mismatches
  Component "major_topic": Lengths (45688, 111) differ (string compare on first 111)
  ── 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 (8839, 22) differ >
  Component "pmid": Numeric: lengths (8839, 22) differ
  Component "list_owner": Lengths (8839, 22) differ (string compare on first 22)
  ── 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 (0, 102) differ >
  Component "pmid": Numeric: lengths (0, 102) differ
  Component "descriptor_pos": Lengths (0, 102) differ (string compare on first 0)
  Component "descriptor_name": Lengths (0, 102) differ (string compare on first 0)
  Component "descriptor_ui": Lengths (0, 102) differ (string compare on first 0)
  Component "descriptor_major_topic": Lengths (0, 102) differ (string compare on first 0)
  ── 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 (15432, 15) differ >
  Component "pmid": Numeric: lengths (15432, 15) differ
  Component "indexing_method": Lengths (15432, 15) differ (string compare on first 15)
  Component "indexing_method": 2 string mismatches
  ── 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 (0, 28) differ >
  Component "pmid": Numeric: lengths (0, 28) differ
  Component "descriptor_pos": Lengths (0, 28) differ (string compare on first 0)
  Component "qualifier_name": Lengths (0, 28) differ (string compare on first 0)
  Component "qualifier_ui": Lengths (0, 28) differ (string compare on first 0)
  Component "qualifier_major_topic": Lengths (0, 28) differ (string compare on first 0)
  ── 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 (321, 2) differ >
  Component "pmid": Numeric: lengths (321, 2) differ
  Component "text": Lengths (321, 2) differ (string compare on first 2)
  Component "text": 2 string mismatches
  Component "type": Lengths (321, 2) differ (string compare on first 2)
  Component "language": Lengths (321, 2) differ (string compare on first 2)
  Component "language": 2 string mismatches
  ── 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 (15432, 32) differ >
  Component "pmid": Numeric: lengths (15432, 32) differ
  Component "version": Numeric: lengths (15432, 32) differ
  Component "xml_filename": Lengths (15432, 32) differ (string compare on first 32)
  Component "xml_filename": 32 string mismatches
  Component "status": Lengths (15432, 32) differ (string compare on first 32)
  Component "status": 22 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 (68311, 146) differ >
  Component "pmid": Numeric: lengths (68311, 146) differ
  Component "pub_status": Lengths (68311, 146) differ (string compare on first 146)
  Component "pub_status": 119 string mismatches
  Component "pub_date": Numeric: lengths (68311, 146) 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 (16814, 41) differ >
  Component "pmid": Numeric: lengths (16814, 41) differ
  Component "type_name": Lengths (16814, 41) differ (string compare on first 41)
  Component "type_name": 15 string mismatches
  Component "type_id": Lengths (16814, 41) differ (string compare on first 41)
  Component "type_id": 15 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 (24300, 102) differ >
  Component "pmid": Numeric: lengths (24300, 102) differ
  Component "text": Lengths (24300, 102) differ (string compare on first 102)
  Component "text": 23 string mismatches
  Component "label": Lengths (24300, 102) differ (string compare on first 102)
  Component "label": 'is.NA' value mismatch: 21 in current 37 in target
  Component "nlm_category": Lengths (24300, 102) differ (string compare on first 102)
  Component "nlm_category": 'is.NA' value mismatch: 33 in current 49 in target
  Component "abstract_pos": Numeric: lengths (24300, 102) 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 (457, 34) differ >
  Component "pmid": Numeric: lengths (457, 34) differ
  Component "copyright": Lengths (457, 34) differ (string compare on first 34)
  Component "copyright": 9 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 (30032, 55) differ >
  Component "pmid": Numeric: lengths (30032, 55) differ
  Component "title": Lengths (30032, 55) differ (string compare on first 55)
  Component "title": 23 string mismatches
  Component "language": Lengths (30032, 55) differ (string compare on first 55)
  Component "language": 3 string mismatches
  Component "vernacular_title": Lengths (30032, 55) differ (string compare on first 55)
  Component "vernacular_title": 'is.NA' value mismatch: 53 in current 51 in target
  Component "pub_model": Lengths (30032, 55) differ (string compare on first 55)
  ...
  ── 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 (27365, 67) differ >
  Component "pmid": Numeric: lengths (27365, 67) differ
  Component "id_type": Lengths (27365, 67) differ (string compare on first 67)
  Component "id_type": 9 string mismatches
  Component "id_value": Lengths (27365, 67) differ (string compare on first 67)
  Component "id_value": 23 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 (114633, 321) differ >
  Component "pmid": Numeric: lengths (114633, 321) differ
  Component "author_pos": Numeric: lengths (114633, 321) differ
  Component "last_name": Lengths (114633, 321) differ (string compare on first 321)
  Component "last_name": 'is.NA' value mismatch: 4 in current 3 in target
  Component "fore_name": Lengths (114633, 321) differ (string compare on first 321)
  Component "fore_name": 'is.NA' value mismatch: 4 in current 3 in target
  Component "initials": Lengths (114633, 321) differ (string compare on first 321)
  Component "initials": 'is.NA' value mismatch: 4 in current 3 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 (19443, 372) differ >
  Component "pmid": Numeric: lengths (19443, 372) differ
  Component "author_pos": Numeric: lengths (19443, 372) differ
  Component "affiliation_pos": Numeric: lengths (19443, 372) differ
  Component "affiliation": Lengths (19443, 372) differ (string compare on first 372)
  Component "affiliation": 98 string mismatches
  ── 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 (35, 63) differ >
  Component "pmid": Numeric: lengths (35, 63) differ
  Component "author_pos": Numeric: lengths (35, 63) differ
  Component "source": Lengths (35, 63) differ (string compare on first 35)
  Component "identifier": Lengths (35, 63) differ (string compare on first 35)
  Component "identifier": 2 string mismatches
  ── 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 (29755, 43) differ >
  Component "pmid": Numeric: lengths (29755, 43) differ
  Component "complete": Lengths (29755, 43) differ (string compare on first 43)
  ── 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 (146717, 17) differ >
  Component "pmid": Numeric: lengths (146717, 17) differ
  Component "registry_number": Lengths (146717, 17) differ (string compare on first 17)
  Component "substance_name": Lengths (146717, 17) differ (string compare on first 17)
  Component "substance_ui": Lengths (146717, 17) differ (string compare on first 17)
  ── 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 (1031, 4) differ >
  Component "pmid": Numeric: lengths (1031, 4) differ
  Component "ref_type": Lengths (1031, 4) differ (string compare on first 4)
  Component "ref_type": 2 string mismatches
  Component "ref_pmid": Numeric: lengths (1031, 4) 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 (6623, 7) differ >
  Component "pmid": Numeric: lengths (6623, 7) differ
  Component "data_bank_name": Lengths (6623, 7) differ (string compare on first 7)
  Component "data_bank_name": 2 string mismatches
  Component "accession_number": Lengths (6623, 7) differ (string compare on first 7)
  Component "accession_number": 2 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 (6986, 13) differ >
  Component "pmid": Numeric: lengths (6986, 13) differ
  Component "grant_id": Lengths (6986, 13) differ (string compare on first 13)
  Component "grant_id": 10 string mismatches
  Component "acronym": Lengths (6986, 13) differ (string compare on first 13)
  Component "acronym": 'is.NA' value mismatch: 13 in current 4 in target
  Component "agency": Lengths (6986, 13) differ (string compare on first 13)
  Component "agency": 10 string mismatches
  Component "country": Lengths (6986, 13) differ (string compare on first 13)
  ...
  ── 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 (4053, 5) differ >
  Component "pmid": Numeric: lengths (4053, 5) differ
  Component "complete": Lengths (4053, 5) differ (string compare on first 5)
  ── 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 (169, 152) differ >
  Component "pmid": Numeric: lengths (169, 152) differ
  Component "investigator_pos": Numeric: lengths (169, 152) differ
  Component "last_name": Lengths (169, 152) differ (string compare on first 152)
  Component "fore_name": Lengths (169, 152) differ (string compare on first 152)
  Component "initials": Lengths (169, 152) differ (string compare on first 152)
  Component "suffix": Lengths (169, 152) differ (string compare on first 152)
  Component "valid": Lengths (169, 152) differ (string compare on first 152)
  ── 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 (17, 0) differ >
  Component "pmid": Numeric: lengths (17, 0) differ
  Component "investigator_pos": Numeric: lengths (17, 0) differ
  Component "affiliation_pos": Numeric: lengths (17, 0) differ
  Component "affiliation": Lengths (17, 0) differ (string compare on first 0)
  ── 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 (30032, 55) differ >
  Component "pmid": Numeric: lengths (30032, 55) differ
  Component "journal_name": Lengths (30032, 55) differ (string compare on first 55)
  Component "journal_name": 23 string mismatches
  Component "journal_iso": Lengths (30032, 55) differ (string compare on first 55)
  Component "journal_iso": 23 string mismatches
  Component "pub_date": Numeric: lengths (30032, 55) differ
  Component "pub_year": Lengths (30032, 55) differ (string compare on first 55)
  Component "pub_year": 23 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 (727, 137) differ >
  Component "pmid": Numeric: lengths (727, 137) differ
  Component "keyword_name": Lengths (727, 137) differ (string compare on first 137)
  Component "keyword_name": 26 string mismatches
  Component "major_topic": Lengths (727, 137) differ (string compare on first 137)
  Component "major_topic": 8 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 (91, 27) differ >
  Component "pmid": Numeric: lengths (91, 27) differ
  Component "list_owner": Lengths (91, 27) differ (string compare on first 27)
  Component "list_owner": 5 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 (411623, 102) differ >
  Component "pmid": Numeric: lengths (411623, 102) differ
  Component "descriptor_pos": Lengths (411623, 102) differ (string compare on first 102)
  Component "descriptor_name": Lengths (411623, 102) differ (string compare on first 102)
  Component "descriptor_ui": Lengths (411623, 102) differ (string compare on first 102)
  Component "descriptor_major_topic": Lengths (411623, 102) differ (string compare on first 102)
  ── 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 (38, 15) differ >
  Component "pmid": Numeric: lengths (38, 15) differ
  Component "indexing_method": Lengths (38, 15) differ (string compare on first 15)
  ── 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 (227872, 28) differ >
  Component "pmid": Numeric: lengths (227872, 28) differ
  Component "descriptor_pos": Lengths (227872, 28) differ (string compare on first 28)
  Component "qualifier_name": Lengths (227872, 28) differ (string compare on first 28)
  Component "qualifier_ui": Lengths (227872, 28) differ (string compare on first 28)
  Component "qualifier_major_topic": Lengths (227872, 28) differ (string compare on first 28)
  ── 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 (21, 3) differ >
  Component "pmid": Numeric: lengths (21, 3) differ
  Component "text": Lengths (21, 3) differ (string compare on first 3)
  Component "text": 1 string mismatch
  Component "type": Lengths (21, 3) differ (string compare on first 3)
  Component "type": 1 string mismatch
  Component "language": Lengths (21, 3) differ (string compare on first 3)
  ── 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 (214, 0) differ >
  Component "pmid": Numeric: lengths (214, 0) differ
  Component "source": Lengths (214, 0) differ (string compare on first 0)
  Component "id_value": Lengths (214, 0) differ (string compare on first 0)
  ── 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 (30461, 55) differ >
  Component "pmid": Numeric: lengths (30461, 55) differ
  Component "version": Numeric: lengths (30461, 55) differ
  Component "xml_filename": Lengths (30461, 55) differ (string compare on first 55)
  Component "xml_filename": 23 string mismatches
  Component "status": Lengths (30461, 55) differ (string compare on first 55)
  Component "status": 23 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 (90166, 246) differ >
  Component "pmid": Numeric: lengths (90166, 246) differ
  Component "pub_status": Lengths (90166, 246) differ (string compare on first 246)
  Component "pub_status": 82 string mismatches
  Component "pub_date": Numeric: lengths (90166, 246) 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 (57394, 65) differ >
  Component "pmid": Numeric: lengths (57394, 65) differ
  Component "type_name": Lengths (57394, 65) differ (string compare on first 65)
  Component "type_name": 8 string mismatches
  Component "type_id": Lengths (57394, 65) differ (string compare on first 65)
  Component "type_id": 8 string mismatches
  
  [ FAIL 55 | WARN 0 | SKIP 4 | PASS 132 ]
  Error: Test failures
  Execution halted