Last updated on 2026-01-31 12:50:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.23 | 5.40 | 57.22 | 62.62 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.23 | 3.91 | 148.26 | 152.17 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.23 | 8.00 | 84.35 | 92.35 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.23 | 8.00 | 96.95 | 104.95 | OK | |
| r-devel-windows-x86_64 | 1.0.23 | 7.00 | 74.00 | 81.00 | OK | |
| r-patched-linux-x86_64 | 1.0.23 | 5.31 | 50.22 | 55.53 | OK | |
| r-release-linux-x86_64 | 1.0.23 | 4.65 | 50.11 | 54.76 | OK | |
| r-release-macos-arm64 | 1.0.23 | 1.00 | 51.00 | 52.00 | OK | |
| r-release-macos-x86_64 | 1.0.23 | 4.00 | 103.00 | 107.00 | OK | |
| r-release-windows-x86_64 | 1.0.23 | 6.00 | 74.00 | 80.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.23 | 1.00 | 49.00 | 50.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.23 | 4.00 | 136.00 | 140.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.23 | 8.00 | 88.00 | 96.00 | OK |
Version: 1.0.23
Check: tests
Result: ERROR
Running ‘testthat.R’ [118s/160s]
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//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
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-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-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_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_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
[ FAIL 51 | WARN 2 | SKIP 4 | PASS 136 ]
══ 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 (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 (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 article to equal `DBI::dbReadTable(conExp, tableName)`.
Differences:
Attributes: < Component "row.names": Numeric: lengths (30, 60) differ >
Component "pmid": Numeric: lengths (30, 60) differ
Component "title": Lengths (30, 60) differ (string compare on first 30)
Component "language": Lengths (30, 60) differ (string compare on first 30)
Component "vernacular_title": Lengths (30, 60) differ (string compare on first 30)
Component "pub_model": Lengths (30, 60) differ (string compare on first 30)
Component "pub_date": Numeric: lengths (30, 60) differ
── 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 (40, 76) differ >
Component "pmid": Numeric: lengths (40, 76) differ
Component "id_type": Lengths (40, 76) differ (string compare on first 40)
Component "id_value": Lengths (40, 76) differ (string compare on first 40)
── 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 chemical to equal `DBI::dbReadTable(conExp, tableName)`.
Differences:
Attributes: < Component "row.names": Numeric: lengths (5, 16) differ >
Component "pmid": Numeric: lengths (5, 16) differ
Component "registry_number": Lengths (5, 16) differ (string compare on first 5)
Component "substance_name": Lengths (5, 16) differ (string compare on first 5)
Component "substance_ui": Lengths (5, 16) differ (string compare on first 5)
── 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 (3, 6) differ >
Component "pmid": Numeric: lengths (3, 6) differ
Component "ref_type": Lengths (3, 6) differ (string compare on first 3)
Component "ref_pmid": Numeric: lengths (3, 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 (4, 6) differ >
Component "pmid": Numeric: lengths (4, 6) differ
Component "data_bank_name": Lengths (4, 6) differ (string compare on first 4)
Component "accession_number": Lengths (4, 6) differ (string compare on first 4)
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
Expected grant_item to equal `DBI::dbReadTable(conExp, tableName)`.
Differences:
Attributes: < Component "row.names": Numeric: lengths (35, 57) differ >
Component "pmid": Numeric: lengths (35, 57) differ
Component "grant_id": Lengths (35, 57) differ (string compare on first 35)
Component "acronym": Lengths (35, 57) differ (string compare on first 35)
Component "agency": Lengths (35, 57) differ (string compare on first 35)
Component "country": Lengths (35, 57) differ (string compare on first 35)
── 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 (8, 17) differ >
Component "pmid": Numeric: lengths (8, 17) differ
Component "complete": Lengths (8, 17) differ (string compare on first 8)
── 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 journal to equal `DBI::dbReadTable(conExp, tableName)`.
Differences:
Attributes: < Component "row.names": Numeric: lengths (30, 60) differ >
Component "pmid": Numeric: lengths (30, 60) differ
Component "journal_name": Lengths (30, 60) differ (string compare on first 30)
Component "journal_iso": Lengths (30, 60) differ (string compare on first 30)
Component "pub_date": Numeric: lengths (30, 60) differ
Component "pub_year": Lengths (30, 60) differ (string compare on first 30)
Component "pub_month": Lengths (30, 60) differ (string compare on first 30)
Component "pub_day": Lengths (30, 60) differ (string compare on first 30)
Component "medline_date": Lengths (30, 60) differ (string compare on first 30)
...
── 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 (109, 229) differ >
Component "pmid": Numeric: lengths (109, 229) differ
Component "keyword_name": Lengths (109, 229) differ (string compare on first 109)
Component "major_topic": Lengths (109, 229) differ (string compare on first 109)
── 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 (21, 43) differ >
Component "pmid": Numeric: lengths (21, 43) differ
Component "list_owner": Lengths (21, 43) differ (string compare on first 21)
── 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)
── 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 (4, 7) differ >
Component "pmid": Numeric: lengths (4, 7) differ
Component "text": Lengths (4, 7) differ (string compare on first 4)
Component "type": Lengths (4, 7) differ (string compare on first 4)
Component "language": Lengths (4, 7) differ (string compare on first 4)
── 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 (30, 60) differ >
Component "pmid": Numeric: lengths (30, 60) differ
Component "version": Numeric: lengths (30, 60) differ
Component "xml_filename": Lengths (30, 60) differ (string compare on first 30)
Component "status": Lengths (30, 60) differ (string compare on first 30)
── 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 (143, 293) differ >
Component "pmid": Numeric: lengths (143, 293) differ
Component "pub_status": Lengths (143, 293) differ (string compare on first 143)
Component "pub_date": Numeric: lengths (143, 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 (37, 74) differ >
Component "pmid": Numeric: lengths (37, 74) differ
Component "type_name": Lengths (37, 74) differ (string compare on first 37)
Component "type_id": Lengths (37, 74) differ (string compare on first 37)
[ FAIL 51 | WARN 2 | SKIP 4 | PASS 136 ]
Error:
! Test failures.
Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc