Running ‘testthat.R’ [30s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmparser)
  > 
  > test_check('pmparser')
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-34.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_modify_pubmed_db_std-54.R
  Saving _problems/test_parse_element-46.R
  Saving _problems/test_parse_element-76.R
  Saving _problems/test_parse_element-81.R
  Saving _problems/test_parse_element-86.R
  [ FAIL 25 | WARN 0 | SKIP 4 | PASS 162 ]
  
  ══ 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_std.R:32:5'): modifyPubmedDb create matches standard ──
  Expected abstract to equal `DBI::dbReadTable(conExp, tableName)`.
  Differences:
  Attributes: < Component "row.names": Numeric: lengths (0, 68) differ >
  Component "pmid": Numeric: lengths (0, 68) differ
  Component "text": Lengths (0, 68) differ (string compare on first 0)
  Component "label": Lengths (0, 68) differ (string compare on first 0)
  Component "nlm_category": Lengths (0, 68) differ (string compare on first 0)
  Component "abstract_pos": Numeric: lengths (0, 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 (0, 22) differ >
  Component "pmid": Numeric: lengths (0, 22) differ
  Component "copyright": Lengths (0, 22) differ (string compare on first 0)
  ── 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 (0, 279) differ >
  Component "pmid": Numeric: lengths (0, 279) differ
  Component "author_pos": Numeric: lengths (0, 279) differ
  Component "last_name": Lengths (0, 279) differ (string compare on first 0)
  Component "fore_name": Lengths (0, 279) differ (string compare on first 0)
  Component "initials": Lengths (0, 279) differ (string compare on first 0)
  Component "suffix": Lengths (0, 279) differ (string compare on first 0)
  Component "valid": Lengths (0, 279) differ (string compare on first 0)
  Component "equal_contrib": Lengths (0, 279) differ (string compare on first 0)
  ...
  ── 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 (0, 337) differ >
  Component "pmid": Numeric: lengths (0, 337) differ
  Component "author_pos": Numeric: lengths (0, 337) differ
  Component "affiliation_pos": Numeric: lengths (0, 337) differ
  Component "affiliation": Lengths (0, 337) 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 (0, 29) differ >
  Component "pmid": Numeric: lengths (0, 29) differ
  Component "author_pos": Numeric: lengths (0, 29) differ
  Component "source": Lengths (0, 29) differ (string compare on first 0)
  Component "identifier": Lengths (0, 29) differ (string compare on first 0)
  ── 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 (0, 30) differ >
  Component "pmid": Numeric: lengths (0, 30) differ
  Component "complete": Lengths (0, 30) differ (string compare on first 0)
  ── 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 (0, 80) differ >
  Component "pmid": Numeric: lengths (0, 80) differ
  Component "investigator_pos": Numeric: lengths (0, 80) differ
  Component "last_name": Lengths (0, 80) differ (string compare on first 0)
  Component "fore_name": Lengths (0, 80) differ (string compare on first 0)
  Component "initials": Lengths (0, 80) differ (string compare on first 0)
  Component "suffix": Lengths (0, 80) differ (string compare on first 0)
  Component "valid": Lengths (0, 80) differ (string compare on first 0)
  ── 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 (0, 53) differ >
  Component "pmid": Numeric: lengths (0, 53) differ
  Component "investigator_pos": Numeric: lengths (0, 53) differ
  Component "affiliation_pos": Numeric: lengths (0, 53) differ
  Component "affiliation": Lengths (0, 53) differ (string compare on first 0)
  ── 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 (0, 74) differ >
  Component "pmid": Numeric: lengths (0, 74) differ
  Component "descriptor_pos": Lengths (0, 74) differ (string compare on first 0)
  Component "descriptor_name": Lengths (0, 74) differ (string compare on first 0)
  Component "descriptor_ui": Lengths (0, 74) differ (string compare on first 0)
  Component "descriptor_major_topic": Lengths (0, 74) differ (string compare on first 0)
  ── 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 (0, 30) differ >
  Component "pmid": Numeric: lengths (0, 30) differ
  Component "indexing_method": Lengths (0, 30) differ (string compare on first 0)
  ── 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 (0, 39) differ >
  Component "pmid": Numeric: lengths (0, 39) differ
  Component "descriptor_pos": Lengths (0, 39) differ (string compare on first 0)
  Component "qualifier_name": Lengths (0, 39) differ (string compare on first 0)
  Component "qualifier_ui": Lengths (0, 39) differ (string compare on first 0)
  Component "qualifier_major_topic": Lengths (0, 39) differ (string compare on first 0)
  ── 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 (68, 126) differ >
  Component "pmid": Numeric: lengths (68, 126) differ
  Component "text": Lengths (68, 126) differ (string compare on first 68)
  Component "label": Lengths (68, 126) differ (string compare on first 68)
  Component "nlm_category": Lengths (68, 126) differ (string compare on first 68)
  Component "abstract_pos": Numeric: lengths (68, 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 (22, 43) differ >
  Component "pmid": Numeric: lengths (22, 43) differ
  Component "copyright": Lengths (22, 43) differ (string compare on first 22)
  ── 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 (279, 490) differ >
  Component "pmid": Numeric: lengths (279, 490) differ
  Component "author_pos": Numeric: lengths (279, 490) differ
  Component "last_name": Lengths (279, 490) differ (string compare on first 279)
  Component "fore_name": Lengths (279, 490) differ (string compare on first 279)
  Component "initials": Lengths (279, 490) differ (string compare on first 279)
  Component "suffix": Lengths (279, 490) differ (string compare on first 279)
  Component "valid": Lengths (279, 490) differ (string compare on first 279)
  Component "equal_contrib": Lengths (279, 490) differ (string compare on first 279)
  ...
  ── 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 (337, 614) differ >
  Component "pmid": Numeric: lengths (337, 614) differ
  Component "author_pos": Numeric: lengths (337, 614) differ
  Component "affiliation_pos": Numeric: lengths (337, 614) differ
  Component "affiliation": Lengths (337, 614) differ (string compare on first 337)
  ── 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 (29, 61) differ >
  Component "pmid": Numeric: lengths (29, 61) differ
  Component "author_pos": Numeric: lengths (29, 61) differ
  Component "source": Lengths (29, 61) differ (string compare on first 29)
  Component "identifier": Lengths (29, 61) differ (string compare on first 29)
  ── 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 (30, 59) differ >
  Component "pmid": Numeric: lengths (30, 59) differ
  Component "complete": Lengths (30, 59) differ (string compare on first 30)
  ── 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 (80, 144) differ >
  Component "pmid": Numeric: lengths (80, 144) differ
  Component "investigator_pos": Numeric: lengths (80, 144) differ
  Component "last_name": Lengths (80, 144) differ (string compare on first 80)
  Component "fore_name": Lengths (80, 144) differ (string compare on first 80)
  Component "initials": Lengths (80, 144) differ (string compare on first 80)
  Component "suffix": Lengths (80, 144) differ (string compare on first 80)
  Component "valid": Lengths (80, 144) differ (string compare on first 80)
  ── 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 (74, 140) differ >
  Component "pmid": Numeric: lengths (74, 140) differ
  Component "descriptor_pos": Lengths (74, 140) differ (string compare on first 74)
  Component "descriptor_name": Lengths (74, 140) differ (string compare on first 74)
  Component "descriptor_ui": Lengths (74, 140) differ (string compare on first 74)
  Component "descriptor_major_topic": Lengths (74, 140) differ (string compare on first 74)
  ── 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 (30, 36) differ >
  Component "pmid": Numeric: lengths (30, 36) differ
  Component "indexing_method": Lengths (30, 36) differ (string compare on first 30)
  ── 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 (39, 88) differ >
  Component "pmid": Numeric: lengths (39, 88) differ
  Component "descriptor_pos": Lengths (39, 88) differ (string compare on first 39)
  Component "qualifier_name": Lengths (39, 88) differ (string compare on first 39)
  Component "qualifier_ui": Lengths (39, 88) differ (string compare on first 39)
  Component "qualifier_major_topic": Lengths (39, 88) differ (string compare on first 39)
  ── Error ('test_parse_element.R:46:3'): parseMesh ──────────────────────────────
  Error in ``[.data.table`(x3, , `:=`(descriptor_pos, seq_len(.N)), by = pmid)`: attempt access index 6/6 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─pmparser::parseMesh(pmXml, dPmid) at test_parse_element.R:46:3
   2.   ├─x3[, `:=`(descriptor_pos, seq_len(.N)), by = pmid]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('test_parse_element.R:76:3'): parseAbstract ──────────────────────────
  Error in ``[.data.table`(x5, , `:=`(abstract_pos, seq_len(.N)), by = pmid)`: attempt access index 6/6 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─pmparser::parseAbstract(pmXml, dPmid) at test_parse_element.R:76:3
   2.   ├─x5[, `:=`(abstract_pos, seq_len(.N)), by = pmid]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('test_parse_element.R:81:3'): parseAuthor ────────────────────────────
  Error in ``[.data.table`(dPerson, , `:=`(person_pos, seq_len(.N)), by = pmid)`: attempt access index 9/9 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─pmparser::parseAuthor(pmXml, dPmid) at test_parse_element.R:81:3
   2.   └─pmparser:::parsePerson(pmXml, dPmid, con, tableSuffix, personType = "author")
   3.     ├─dPerson[, `:=`(person_pos, seq_len(.N)), by = pmid]
   4.     └─data.table:::`[.data.table`(...)
  ── Error ('test_parse_element.R:86:3'): parseInvestigator ──────────────────────
  Error in ``[.data.table`(dPerson, , `:=`(person_pos, seq_len(.N)), by = pmid)`: attempt access index 7/7 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─pmparser::parseInvestigator(pmXml, dPmid) at test_parse_element.R:86:3
   2.   └─pmparser:::parsePerson(pmXml, dPmid, con, tableSuffix, personType = "investigator")
   3.     ├─dPerson[, `:=`(person_pos, seq_len(.N)), by = pmid]
   4.     └─data.table:::`[.data.table`(...)
  
  [ FAIL 25 | WARN 0 | SKIP 4 | PASS 162 ]
  Error:
  ! Test failures.
  Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted