CRAN Package Check Results for Package pmparser

Last updated on 2022-12-09 10:00:30 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.13 5.14 63.93 69.07 OK
r-devel-linux-x86_64-debian-gcc 1.0.13 4.40 630.08 634.48 ERROR
r-devel-linux-x86_64-fedora-clang 1.0.13 1148.35 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.13 1029.71 ERROR
r-devel-windows-x86_64 1.0.13 28.00 125.00 153.00 OK
r-patched-linux-x86_64 1.0.13 5.57 59.17 64.74 OK
r-release-linux-x86_64 1.0.13 4.50 60.12 64.62 OK
r-release-macos-arm64 1.0.13 57.00 OK
r-release-macos-x86_64 1.0.13 86.00 OK
r-release-windows-x86_64 1.0.13 15.00 112.00 127.00 OK
r-oldrel-macos-arm64 1.0.13 67.00 OK
r-oldrel-macos-x86_64 1.0.13 77.00 OK
r-oldrel-windows-ix86+x86_64 1.0.13 10.00 88.00 98.00 ERROR

Additional issues

M1mac

Check Details

Version: 1.0.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10m/16m]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(pmparser)
     >
     > test_check('pmparser')
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed23n1166.xml.gz.md5'
     Content type 'unknown' length 60 bytes
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed23n1166.xml.gz'
     Content type 'unknown' length 23756263 bytes (22.7 MB)
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed23n1166.xml.gz.md5'
     Content type 'unknown' length 60 bytes
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed23n1166.xml.gz'
     Content type 'unknown' length 23756263 bytes (22.7 MB)
     ==================================================
     [ FAIL 51 | WARN 0 | SKIP 4 | PASS 136 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (4)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (20847, 57) differ >
     Component "pmid": Numeric: lengths (20847, 57) differ
     Component "text": Lengths (20847, 57) differ (string compare on first 57)
     Component "text": 57 string mismatches
     Component "label": Lengths (20847, 57) differ (string compare on first 57)
     Component "label": 'is.NA' value mismatch: 18 in current 11 in target
     Component "nlm_category": Lengths (20847, 57) differ (string compare on first 57)
     Component "nlm_category": 'is.NA' value mismatch: 30 in current 11 in target
     Component "abstract_pos": Numeric: lengths (20847, 57) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (7392, 19) differ >
     Component "pmid": Numeric: lengths (7392, 19) differ
     Component "copyright": Lengths (7392, 19) differ (string compare on first 19)
     Component "copyright": 19 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     article not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "title": Lengths (10710, 28) differ (string compare on first 28)
     Component "title": 28 string mismatches
     Component "pub_date": Numeric: lengths (10710, 28) differ
     Component "pub_model": Lengths (10710, 28) differ (string compare on first 28)
     Component "pub_model": 12 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     article_id not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (15050, 38) differ >
     Component "pmid": Numeric: lengths (15050, 38) differ
     Component "id_type": Lengths (15050, 38) differ (string compare on first 38)
     Component "id_type": 10 string mismatches
     Component "id_value": Lengths (15050, 38) differ (string compare on first 38)
     Component "id_value": 38 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (66920, 197) differ >
     Component "pmid": Numeric: lengths (66920, 197) differ
     Component "author_pos": Numeric: lengths (66920, 197) differ
     Component "last_name": Lengths (66920, 197) differ (string compare on first 197)
     Component "last_name": 'is.NA' value mismatch: 3 in current 0 in target
     Component "fore_name": Lengths (66920, 197) differ (string compare on first 197)
     Component "fore_name": 'is.NA' value mismatch: 3 in current 0 in target
     Component "initials": Lengths (66920, 197) differ (string compare on first 197)
     Component "initials": 'is.NA' value mismatch: 3 in current 0 in target
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (79745, 218) differ >
     Component "pmid": Numeric: lengths (79745, 218) differ
     Component "author_pos": Numeric: lengths (79745, 218) differ
     Component "affiliation_pos": Numeric: lengths (79745, 218) differ
     Component "affiliation": Lengths (79745, 218) differ (string compare on first 218)
     Component "affiliation": 218 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3808, 0) differ >
     Component "pmid": Numeric: lengths (3808, 0) differ
     Component "author_pos": Numeric: lengths (3808, 0) differ
     Component "affiliation_pos": Numeric: lengths (3808, 0) differ
     Component "source": Lengths (3808, 0) differ (string compare on first 0)
     Component "identifier": Lengths (3808, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10032, 18) differ >
     Component "pmid": Numeric: lengths (10032, 18) differ
     Component "author_pos": Numeric: lengths (10032, 18) differ
     Component "source": Lengths (10032, 18) differ (string compare on first 18)
     Component "identifier": Lengths (10032, 18) differ (string compare on first 18)
     Component "identifier": 18 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10580, 28) differ >
     Component "pmid": Numeric: lengths (10580, 28) differ
     Component "complete": Lengths (10580, 28) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     chemical not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2075, 0) differ >
     Component "pmid": Numeric: lengths (2075, 0) differ
     Component "registry_number": Lengths (2075, 0) differ (string compare on first 0)
     Component "substance_name": Lengths (2075, 0) differ (string compare on first 0)
     Component "substance_ui": Lengths (2075, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     comment not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (250, 3) differ >
     Component "pmid": Numeric: lengths (250, 3) differ
     Component "ref_type": Lengths (250, 3) differ (string compare on first 3)
     Component "ref_type": 3 string mismatches
     Component "ref_pmid": Numeric: lengths (250, 3) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     data_bank not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (214, 4) differ >
     Component "pmid": Numeric: lengths (214, 4) differ
     Component "data_bank_name": Lengths (214, 4) differ (string compare on first 4)
     Component "data_bank_name": 3 string mismatches
     Component "accession_number": Lengths (214, 4) differ (string compare on first 4)
     Component "accession_number": 4 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     grant_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2770, 16) differ >
     Component "pmid": Numeric: lengths (2770, 16) differ
     Component "grant_id": Lengths (2770, 16) differ (string compare on first 16)
     Component "grant_id": 'is.NA' value mismatch: 0 in current 5 in target
     Component "acronym": Lengths (2770, 16) differ (string compare on first 16)
     Component "acronym": 'is.NA' value mismatch: 13 in current 16 in target
     Component "agency": Lengths (2770, 16) differ (string compare on first 16)
     Component "agency": 16 string mismatches
     Component "country": Lengths (2770, 16) differ (string compare on first 16)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     grant_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1042, 6) differ >
     Component "pmid": Numeric: lengths (1042, 6) differ
     Component "complete": Lengths (1042, 6) differ (string compare on first 6)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     investigator not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1434, 27) differ >
     Component "pmid": Numeric: lengths (1434, 27) differ
     Component "investigator_pos": Numeric: lengths (1434, 27) differ
     Component "last_name": Lengths (1434, 27) differ (string compare on first 27)
     Component "last_name": 27 string mismatches
     Component "fore_name": Lengths (1434, 27) differ (string compare on first 27)
     Component "fore_name": 27 string mismatches
     Component "initials": Lengths (1434, 27) differ (string compare on first 27)
     Component "initials": 26 string mismatches
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (73, 0) differ >
     Component "pmid": Numeric: lengths (73, 0) differ
     Component "investigator_pos": Numeric: lengths (73, 0) differ
     Component "affiliation_pos": Numeric: lengths (73, 0) differ
     Component "affiliation": Lengths (73, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     journal not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "journal_name": Lengths (10710, 28) differ (string compare on first 28)
     Component "journal_name": 28 string mismatches
     Component "journal_iso": Lengths (10710, 28) differ (string compare on first 28)
     Component "journal_iso": 28 string mismatches
     Component "pub_date": Numeric: lengths (10710, 28) differ
     Component "pub_year": Lengths (10710, 28) differ (string compare on first 28)
     Component "pub_year": 28 string mismatches
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     keyword_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (41142, 102) differ >
     Component "pmid": Numeric: lengths (41142, 102) differ
     Component "keyword_name": Lengths (41142, 102) differ (string compare on first 102)
     Component "keyword_name": 102 string mismatches
     Component "major_topic": Lengths (41142, 102) differ (string compare on first 102)
     Component "major_topic": 6 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     keyword_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (7781, 20) differ >
     Component "pmid": Numeric: lengths (7781, 20) differ
     Component "list_owner": Lengths (7781, 20) differ (string compare on first 20)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (11553, 0) differ >
     Component "pmid": Numeric: lengths (11553, 0) differ
     Component "descriptor_pos": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_name": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_ui": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_major_topic": Lengths (11553, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1659, 0) differ >
     Component "pmid": Numeric: lengths (1659, 0) differ
     Component "indexing_method": Lengths (1659, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3968, 0) differ >
     Component "pmid": Numeric: lengths (3968, 0) differ
     Component "descriptor_pos": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_name": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_ui": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_major_topic": Lengths (3968, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     other_abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (216, 2) differ >
     Component "pmid": Numeric: lengths (216, 2) differ
     Component "text": Lengths (216, 2) differ (string compare on first 2)
     Component "text": 2 string mismatches
     Component "type": Lengths (216, 2) differ (string compare on first 2)
     Component "type": 1 string mismatch
     Component "language": Lengths (216, 2) differ (string compare on first 2)
     Component "language": 2 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pmid_status not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "version": Numeric: lengths (10710, 28) differ
     Component "xml_filename": Lengths (10710, 28) differ (string compare on first 28)
     Component "xml_filename": 28 string mismatches
     Component "status": Lengths (10710, 28) differ (string compare on first 28)
     Component "status": 15 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pub_history not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (50281, 127) differ >
     Component "pmid": Numeric: lengths (50281, 127) differ
     Component "pub_status": Lengths (50281, 127) differ (string compare on first 127)
     Component "pub_status": 91 string mismatches
     Component "pub_date": Numeric: lengths (50281, 127) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pub_type not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (12429, 30) differ >
     Component "pmid": Numeric: lengths (12429, 30) differ
     Component "type_name": Lengths (12429, 30) differ (string compare on first 30)
     Component "type_name": 13 string mismatches
     Component "type_id": Lengths (12429, 30) differ (string compare on first 30)
     Component "type_id": 13 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): 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'): modifyPubmedDb update matches standard ──
     abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (57, 117) differ >
     Component "pmid": Numeric: lengths (57, 117) differ
     Component "text": Lengths (57, 117) differ (string compare on first 57)
     Component "label": Lengths (57, 117) differ (string compare on first 57)
     Component "nlm_category": Lengths (57, 117) differ (string compare on first 57)
     Component "abstract_pos": Numeric: lengths (57, 117) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (19, 34) differ >
     Component "pmid": Numeric: lengths (19, 34) differ
     Component "copyright": Lengths (19, 34) differ (string compare on first 19)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     article not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "title": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_date": Numeric: lengths (28, 58) differ
     Component "pub_model": Lengths (28, 58) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     article_id not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (38, 76) differ >
     Component "pmid": Numeric: lengths (38, 76) differ
     Component "id_type": Lengths (38, 76) differ (string compare on first 38)
     Component "id_value": Lengths (38, 76) differ (string compare on first 38)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (197, 386) differ >
     Component "pmid": Numeric: lengths (197, 386) differ
     Component "author_pos": Numeric: lengths (197, 386) differ
     Component "last_name": Lengths (197, 386) differ (string compare on first 197)
     Component "fore_name": Lengths (197, 386) differ (string compare on first 197)
     Component "initials": Lengths (197, 386) differ (string compare on first 197)
     Component "suffix": Lengths (197, 386) differ (string compare on first 197)
     Component "valid": Lengths (197, 386) differ (string compare on first 197)
     Component "equal_contrib": Lengths (197, 386) differ (string compare on first 197)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (218, 453) differ >
     Component "pmid": Numeric: lengths (218, 453) differ
     Component "author_pos": Numeric: lengths (218, 453) differ
     Component "affiliation_pos": Numeric: lengths (218, 453) differ
     Component "affiliation": Lengths (218, 453) differ (string compare on first 218)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (18, 60) differ >
     Component "pmid": Numeric: lengths (18, 60) differ
     Component "author_pos": Numeric: lengths (18, 60) differ
     Component "source": Lengths (18, 60) differ (string compare on first 18)
     Component "identifier": Lengths (18, 60) differ (string compare on first 18)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "complete": Lengths (28, 58) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     chemical not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 44) differ >
     Component "pmid": Numeric: lengths (0, 44) differ
     Component "registry_number": Lengths (0, 44) differ (string compare on first 0)
     Component "substance_name": Lengths (0, 44) differ (string compare on first 0)
     Component "substance_ui": Lengths (0, 44) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     comment not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3, 8) differ >
     Component "pmid": Numeric: lengths (3, 8) differ
     Component "ref_type": Lengths (3, 8) differ (string compare on first 3)
     Component "ref_pmid": Numeric: lengths (3, 8) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     data_bank not equal to DBI::dbReadTable(conExp, tableName).
     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'): modifyPubmedDb update matches standard ──
     grant_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (16, 34) differ >
     Component "pmid": Numeric: lengths (16, 34) differ
     Component "grant_id": Lengths (16, 34) differ (string compare on first 16)
     Component "acronym": Lengths (16, 34) differ (string compare on first 16)
     Component "agency": Lengths (16, 34) differ (string compare on first 16)
     Component "country": Lengths (16, 34) differ (string compare on first 16)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     grant_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (6, 12) differ >
     Component "pmid": Numeric: lengths (6, 12) differ
     Component "complete": Lengths (6, 12) differ (string compare on first 6)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     investigator not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (27, 54) differ >
     Component "pmid": Numeric: lengths (27, 54) differ
     Component "investigator_pos": Numeric: lengths (27, 54) differ
     Component "last_name": Lengths (27, 54) differ (string compare on first 27)
     Component "fore_name": Lengths (27, 54) differ (string compare on first 27)
     Component "initials": Lengths (27, 54) differ (string compare on first 27)
     Component "suffix": Lengths (27, 54) differ (string compare on first 27)
     Component "valid": Lengths (27, 54) differ (string compare on first 27)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     journal not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "journal_name": Lengths (28, 58) differ (string compare on first 28)
     Component "journal_iso": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_date": Numeric: lengths (28, 58) differ
     Component "pub_year": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_month": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_day": Lengths (28, 58) differ (string compare on first 28)
     Component "medline_date": Lengths (28, 58) differ (string compare on first 28)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     keyword_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (102, 195) differ >
     Component "pmid": Numeric: lengths (102, 195) differ
     Component "keyword_name": Lengths (102, 195) differ (string compare on first 102)
     Component "major_topic": Lengths (102, 195) differ (string compare on first 102)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     keyword_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (20, 39) differ >
     Component "pmid": Numeric: lengths (20, 39) differ
     Component "list_owner": Lengths (20, 39) differ (string compare on first 20)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 256) differ >
     Component "pmid": Numeric: lengths (0, 256) differ
     Component "descriptor_pos": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_name": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_ui": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_major_topic": Lengths (0, 256) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 13) differ >
     Component "pmid": Numeric: lengths (0, 13) differ
     Component "indexing_method": Lengths (0, 13) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 152) differ >
     Component "pmid": Numeric: lengths (0, 152) differ
     Component "descriptor_pos": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_name": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_ui": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_major_topic": Lengths (0, 152) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     other_abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2, 4) differ >
     Component "pmid": Numeric: lengths (2, 4) differ
     Component "text": Lengths (2, 4) differ (string compare on first 2)
     Component "type": Lengths (2, 4) differ (string compare on first 2)
     Component "language": Lengths (2, 4) differ (string compare on first 2)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pmid_status not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 106) differ >
     Component "pmid": Numeric: lengths (28, 106) differ
     Component "version": Numeric: lengths (28, 106) differ
     Component "xml_filename": Lengths (28, 106) differ (string compare on first 28)
     Component "status": Lengths (28, 106) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pub_history not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (127, 254) differ >
     Component "pmid": Numeric: lengths (127, 254) differ
     Component "pub_status": Lengths (127, 254) differ (string compare on first 127)
     Component "pub_date": Numeric: lengths (127, 254) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pub_type not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (30, 79) differ >
     Component "pmid": Numeric: lengths (30, 79) differ
     Component "type_name": Lengths (30, 79) differ (string compare on first 30)
     Component "type_id": Lengths (30, 79) differ (string compare on first 30)
    
     [ FAIL 51 | WARN 0 | SKIP 4 | PASS 136 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [18m/18m]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(pmparser)
     >
     > test_check('pmparser')
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed23n1166.xml.gz.md5'
     Content type 'unknown' length 60 bytes
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed23n1166.xml.gz'
     Content type 'unknown' length 23756263 bytes (22.7 MB)
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed23n1166.xml.gz.md5'
     Content type 'unknown' length 60 bytes
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed23n1166.xml.gz'
     Content type 'unknown' length 23756263 bytes (22.7 MB)
     ==================================================
     [ FAIL 51 | WARN 0 | SKIP 4 | PASS 136 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (4)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (20847, 57) differ >
     Component "pmid": Numeric: lengths (20847, 57) differ
     Component "text": Lengths (20847, 57) differ (string compare on first 57)
     Component "text": 57 string mismatches
     Component "label": Lengths (20847, 57) differ (string compare on first 57)
     Component "label": 'is.NA' value mismatch: 18 in current 11 in target
     Component "nlm_category": Lengths (20847, 57) differ (string compare on first 57)
     Component "nlm_category": 'is.NA' value mismatch: 30 in current 11 in target
     Component "abstract_pos": Numeric: lengths (20847, 57) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (7392, 19) differ >
     Component "pmid": Numeric: lengths (7392, 19) differ
     Component "copyright": Lengths (7392, 19) differ (string compare on first 19)
     Component "copyright": 19 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     article not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "title": Lengths (10710, 28) differ (string compare on first 28)
     Component "title": 28 string mismatches
     Component "pub_date": Numeric: lengths (10710, 28) differ
     Component "pub_model": Lengths (10710, 28) differ (string compare on first 28)
     Component "pub_model": 12 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     article_id not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (15050, 38) differ >
     Component "pmid": Numeric: lengths (15050, 38) differ
     Component "id_type": Lengths (15050, 38) differ (string compare on first 38)
     Component "id_type": 10 string mismatches
     Component "id_value": Lengths (15050, 38) differ (string compare on first 38)
     Component "id_value": 38 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (66920, 197) differ >
     Component "pmid": Numeric: lengths (66920, 197) differ
     Component "author_pos": Numeric: lengths (66920, 197) differ
     Component "last_name": Lengths (66920, 197) differ (string compare on first 197)
     Component "last_name": 'is.NA' value mismatch: 3 in current 0 in target
     Component "fore_name": Lengths (66920, 197) differ (string compare on first 197)
     Component "fore_name": 'is.NA' value mismatch: 3 in current 0 in target
     Component "initials": Lengths (66920, 197) differ (string compare on first 197)
     Component "initials": 'is.NA' value mismatch: 3 in current 0 in target
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (79745, 218) differ >
     Component "pmid": Numeric: lengths (79745, 218) differ
     Component "author_pos": Numeric: lengths (79745, 218) differ
     Component "affiliation_pos": Numeric: lengths (79745, 218) differ
     Component "affiliation": Lengths (79745, 218) differ (string compare on first 218)
     Component "affiliation": 218 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3808, 0) differ >
     Component "pmid": Numeric: lengths (3808, 0) differ
     Component "author_pos": Numeric: lengths (3808, 0) differ
     Component "affiliation_pos": Numeric: lengths (3808, 0) differ
     Component "source": Lengths (3808, 0) differ (string compare on first 0)
     Component "identifier": Lengths (3808, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10032, 18) differ >
     Component "pmid": Numeric: lengths (10032, 18) differ
     Component "author_pos": Numeric: lengths (10032, 18) differ
     Component "source": Lengths (10032, 18) differ (string compare on first 18)
     Component "identifier": Lengths (10032, 18) differ (string compare on first 18)
     Component "identifier": 18 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10580, 28) differ >
     Component "pmid": Numeric: lengths (10580, 28) differ
     Component "complete": Lengths (10580, 28) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     chemical not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2075, 0) differ >
     Component "pmid": Numeric: lengths (2075, 0) differ
     Component "registry_number": Lengths (2075, 0) differ (string compare on first 0)
     Component "substance_name": Lengths (2075, 0) differ (string compare on first 0)
     Component "substance_ui": Lengths (2075, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     comment not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (250, 3) differ >
     Component "pmid": Numeric: lengths (250, 3) differ
     Component "ref_type": Lengths (250, 3) differ (string compare on first 3)
     Component "ref_type": 3 string mismatches
     Component "ref_pmid": Numeric: lengths (250, 3) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     data_bank not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (214, 4) differ >
     Component "pmid": Numeric: lengths (214, 4) differ
     Component "data_bank_name": Lengths (214, 4) differ (string compare on first 4)
     Component "data_bank_name": 3 string mismatches
     Component "accession_number": Lengths (214, 4) differ (string compare on first 4)
     Component "accession_number": 4 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     grant_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2770, 16) differ >
     Component "pmid": Numeric: lengths (2770, 16) differ
     Component "grant_id": Lengths (2770, 16) differ (string compare on first 16)
     Component "grant_id": 'is.NA' value mismatch: 0 in current 5 in target
     Component "acronym": Lengths (2770, 16) differ (string compare on first 16)
     Component "acronym": 'is.NA' value mismatch: 13 in current 16 in target
     Component "agency": Lengths (2770, 16) differ (string compare on first 16)
     Component "agency": 16 string mismatches
     Component "country": Lengths (2770, 16) differ (string compare on first 16)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     grant_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1042, 6) differ >
     Component "pmid": Numeric: lengths (1042, 6) differ
     Component "complete": Lengths (1042, 6) differ (string compare on first 6)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     investigator not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1434, 27) differ >
     Component "pmid": Numeric: lengths (1434, 27) differ
     Component "investigator_pos": Numeric: lengths (1434, 27) differ
     Component "last_name": Lengths (1434, 27) differ (string compare on first 27)
     Component "last_name": 27 string mismatches
     Component "fore_name": Lengths (1434, 27) differ (string compare on first 27)
     Component "fore_name": 27 string mismatches
     Component "initials": Lengths (1434, 27) differ (string compare on first 27)
     Component "initials": 26 string mismatches
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (73, 0) differ >
     Component "pmid": Numeric: lengths (73, 0) differ
     Component "investigator_pos": Numeric: lengths (73, 0) differ
     Component "affiliation_pos": Numeric: lengths (73, 0) differ
     Component "affiliation": Lengths (73, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     journal not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "journal_name": Lengths (10710, 28) differ (string compare on first 28)
     Component "journal_name": 28 string mismatches
     Component "journal_iso": Lengths (10710, 28) differ (string compare on first 28)
     Component "journal_iso": 28 string mismatches
     Component "pub_date": Numeric: lengths (10710, 28) differ
     Component "pub_year": Lengths (10710, 28) differ (string compare on first 28)
     Component "pub_year": 28 string mismatches
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     keyword_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (41142, 102) differ >
     Component "pmid": Numeric: lengths (41142, 102) differ
     Component "keyword_name": Lengths (41142, 102) differ (string compare on first 102)
     Component "keyword_name": 102 string mismatches
     Component "major_topic": Lengths (41142, 102) differ (string compare on first 102)
     Component "major_topic": 6 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     keyword_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (7781, 20) differ >
     Component "pmid": Numeric: lengths (7781, 20) differ
     Component "list_owner": Lengths (7781, 20) differ (string compare on first 20)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (11553, 0) differ >
     Component "pmid": Numeric: lengths (11553, 0) differ
     Component "descriptor_pos": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_name": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_ui": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_major_topic": Lengths (11553, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1659, 0) differ >
     Component "pmid": Numeric: lengths (1659, 0) differ
     Component "indexing_method": Lengths (1659, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3968, 0) differ >
     Component "pmid": Numeric: lengths (3968, 0) differ
     Component "descriptor_pos": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_name": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_ui": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_major_topic": Lengths (3968, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     other_abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (216, 2) differ >
     Component "pmid": Numeric: lengths (216, 2) differ
     Component "text": Lengths (216, 2) differ (string compare on first 2)
     Component "text": 2 string mismatches
     Component "type": Lengths (216, 2) differ (string compare on first 2)
     Component "type": 1 string mismatch
     Component "language": Lengths (216, 2) differ (string compare on first 2)
     Component "language": 2 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pmid_status not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "version": Numeric: lengths (10710, 28) differ
     Component "xml_filename": Lengths (10710, 28) differ (string compare on first 28)
     Component "xml_filename": 28 string mismatches
     Component "status": Lengths (10710, 28) differ (string compare on first 28)
     Component "status": 15 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pub_history not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (50281, 127) differ >
     Component "pmid": Numeric: lengths (50281, 127) differ
     Component "pub_status": Lengths (50281, 127) differ (string compare on first 127)
     Component "pub_status": 91 string mismatches
     Component "pub_date": Numeric: lengths (50281, 127) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pub_type not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (12429, 30) differ >
     Component "pmid": Numeric: lengths (12429, 30) differ
     Component "type_name": Lengths (12429, 30) differ (string compare on first 30)
     Component "type_name": 13 string mismatches
     Component "type_id": Lengths (12429, 30) differ (string compare on first 30)
     Component "type_id": 13 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): 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'): modifyPubmedDb update matches standard ──
     abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (57, 117) differ >
     Component "pmid": Numeric: lengths (57, 117) differ
     Component "text": Lengths (57, 117) differ (string compare on first 57)
     Component "label": Lengths (57, 117) differ (string compare on first 57)
     Component "nlm_category": Lengths (57, 117) differ (string compare on first 57)
     Component "abstract_pos": Numeric: lengths (57, 117) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (19, 34) differ >
     Component "pmid": Numeric: lengths (19, 34) differ
     Component "copyright": Lengths (19, 34) differ (string compare on first 19)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     article not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "title": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_date": Numeric: lengths (28, 58) differ
     Component "pub_model": Lengths (28, 58) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     article_id not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (38, 76) differ >
     Component "pmid": Numeric: lengths (38, 76) differ
     Component "id_type": Lengths (38, 76) differ (string compare on first 38)
     Component "id_value": Lengths (38, 76) differ (string compare on first 38)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (197, 386) differ >
     Component "pmid": Numeric: lengths (197, 386) differ
     Component "author_pos": Numeric: lengths (197, 386) differ
     Component "last_name": Lengths (197, 386) differ (string compare on first 197)
     Component "fore_name": Lengths (197, 386) differ (string compare on first 197)
     Component "initials": Lengths (197, 386) differ (string compare on first 197)
     Component "suffix": Lengths (197, 386) differ (string compare on first 197)
     Component "valid": Lengths (197, 386) differ (string compare on first 197)
     Component "equal_contrib": Lengths (197, 386) differ (string compare on first 197)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (218, 453) differ >
     Component "pmid": Numeric: lengths (218, 453) differ
     Component "author_pos": Numeric: lengths (218, 453) differ
     Component "affiliation_pos": Numeric: lengths (218, 453) differ
     Component "affiliation": Lengths (218, 453) differ (string compare on first 218)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (18, 60) differ >
     Component "pmid": Numeric: lengths (18, 60) differ
     Component "author_pos": Numeric: lengths (18, 60) differ
     Component "source": Lengths (18, 60) differ (string compare on first 18)
     Component "identifier": Lengths (18, 60) differ (string compare on first 18)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "complete": Lengths (28, 58) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     chemical not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 44) differ >
     Component "pmid": Numeric: lengths (0, 44) differ
     Component "registry_number": Lengths (0, 44) differ (string compare on first 0)
     Component "substance_name": Lengths (0, 44) differ (string compare on first 0)
     Component "substance_ui": Lengths (0, 44) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     comment not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3, 8) differ >
     Component "pmid": Numeric: lengths (3, 8) differ
     Component "ref_type": Lengths (3, 8) differ (string compare on first 3)
     Component "ref_pmid": Numeric: lengths (3, 8) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     data_bank not equal to DBI::dbReadTable(conExp, tableName).
     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'): modifyPubmedDb update matches standard ──
     grant_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (16, 34) differ >
     Component "pmid": Numeric: lengths (16, 34) differ
     Component "grant_id": Lengths (16, 34) differ (string compare on first 16)
     Component "acronym": Lengths (16, 34) differ (string compare on first 16)
     Component "agency": Lengths (16, 34) differ (string compare on first 16)
     Component "country": Lengths (16, 34) differ (string compare on first 16)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     grant_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (6, 12) differ >
     Component "pmid": Numeric: lengths (6, 12) differ
     Component "complete": Lengths (6, 12) differ (string compare on first 6)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     investigator not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (27, 54) differ >
     Component "pmid": Numeric: lengths (27, 54) differ
     Component "investigator_pos": Numeric: lengths (27, 54) differ
     Component "last_name": Lengths (27, 54) differ (string compare on first 27)
     Component "fore_name": Lengths (27, 54) differ (string compare on first 27)
     Component "initials": Lengths (27, 54) differ (string compare on first 27)
     Component "suffix": Lengths (27, 54) differ (string compare on first 27)
     Component "valid": Lengths (27, 54) differ (string compare on first 27)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     journal not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "journal_name": Lengths (28, 58) differ (string compare on first 28)
     Component "journal_iso": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_date": Numeric: lengths (28, 58) differ
     Component "pub_year": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_month": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_day": Lengths (28, 58) differ (string compare on first 28)
     Component "medline_date": Lengths (28, 58) differ (string compare on first 28)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     keyword_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (102, 195) differ >
     Component "pmid": Numeric: lengths (102, 195) differ
     Component "keyword_name": Lengths (102, 195) differ (string compare on first 102)
     Component "major_topic": Lengths (102, 195) differ (string compare on first 102)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     keyword_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (20, 39) differ >
     Component "pmid": Numeric: lengths (20, 39) differ
     Component "list_owner": Lengths (20, 39) differ (string compare on first 20)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 256) differ >
     Component "pmid": Numeric: lengths (0, 256) differ
     Component "descriptor_pos": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_name": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_ui": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_major_topic": Lengths (0, 256) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 13) differ >
     Component "pmid": Numeric: lengths (0, 13) differ
     Component "indexing_method": Lengths (0, 13) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 152) differ >
     Component "pmid": Numeric: lengths (0, 152) differ
     Component "descriptor_pos": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_name": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_ui": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_major_topic": Lengths (0, 152) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     other_abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2, 4) differ >
     Component "pmid": Numeric: lengths (2, 4) differ
     Component "text": Lengths (2, 4) differ (string compare on first 2)
     Component "type": Lengths (2, 4) differ (string compare on first 2)
     Component "language": Lengths (2, 4) differ (string compare on first 2)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pmid_status not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 106) differ >
     Component "pmid": Numeric: lengths (28, 106) differ
     Component "version": Numeric: lengths (28, 106) differ
     Component "xml_filename": Lengths (28, 106) differ (string compare on first 28)
     Component "status": Lengths (28, 106) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pub_history not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (127, 254) differ >
     Component "pmid": Numeric: lengths (127, 254) differ
     Component "pub_status": Lengths (127, 254) differ (string compare on first 127)
     Component "pub_date": Numeric: lengths (127, 254) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pub_type not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (30, 79) differ >
     Component "pmid": Numeric: lengths (30, 79) differ
     Component "type_name": Lengths (30, 79) differ (string compare on first 30)
     Component "type_id": Lengths (30, 79) differ (string compare on first 30)
    
     [ FAIL 51 | WARN 0 | SKIP 4 | PASS 136 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [16m/16m]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(pmparser)
     >
     > test_check('pmparser')
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed23n1166.xml.gz.md5'
     Content type 'unknown' length 60 bytes
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed23n1166.xml.gz'
     Content type 'unknown' length 23756263 bytes (22.7 MB)
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed23n1166.xml.gz.md5'
     Content type 'unknown' length 60 bytes
     ==================================================
     trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed23n1166.xml.gz'
     Content type 'unknown' length 23756263 bytes (22.7 MB)
     ==================================================
     [ FAIL 51 | WARN 0 | SKIP 4 | PASS 136 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (4)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (20847, 57) differ >
     Component "pmid": Numeric: lengths (20847, 57) differ
     Component "text": Lengths (20847, 57) differ (string compare on first 57)
     Component "text": 57 string mismatches
     Component "label": Lengths (20847, 57) differ (string compare on first 57)
     Component "label": 'is.NA' value mismatch: 18 in current 11 in target
     Component "nlm_category": Lengths (20847, 57) differ (string compare on first 57)
     Component "nlm_category": 'is.NA' value mismatch: 30 in current 11 in target
     Component "abstract_pos": Numeric: lengths (20847, 57) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (7392, 19) differ >
     Component "pmid": Numeric: lengths (7392, 19) differ
     Component "copyright": Lengths (7392, 19) differ (string compare on first 19)
     Component "copyright": 19 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     article not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "title": Lengths (10710, 28) differ (string compare on first 28)
     Component "title": 28 string mismatches
     Component "pub_date": Numeric: lengths (10710, 28) differ
     Component "pub_model": Lengths (10710, 28) differ (string compare on first 28)
     Component "pub_model": 12 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     article_id not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (15050, 38) differ >
     Component "pmid": Numeric: lengths (15050, 38) differ
     Component "id_type": Lengths (15050, 38) differ (string compare on first 38)
     Component "id_type": 10 string mismatches
     Component "id_value": Lengths (15050, 38) differ (string compare on first 38)
     Component "id_value": 38 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (66920, 197) differ >
     Component "pmid": Numeric: lengths (66920, 197) differ
     Component "author_pos": Numeric: lengths (66920, 197) differ
     Component "last_name": Lengths (66920, 197) differ (string compare on first 197)
     Component "last_name": 'is.NA' value mismatch: 3 in current 0 in target
     Component "fore_name": Lengths (66920, 197) differ (string compare on first 197)
     Component "fore_name": 'is.NA' value mismatch: 3 in current 0 in target
     Component "initials": Lengths (66920, 197) differ (string compare on first 197)
     Component "initials": 'is.NA' value mismatch: 3 in current 0 in target
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (79745, 218) differ >
     Component "pmid": Numeric: lengths (79745, 218) differ
     Component "author_pos": Numeric: lengths (79745, 218) differ
     Component "affiliation_pos": Numeric: lengths (79745, 218) differ
     Component "affiliation": Lengths (79745, 218) differ (string compare on first 218)
     Component "affiliation": 218 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3808, 0) differ >
     Component "pmid": Numeric: lengths (3808, 0) differ
     Component "author_pos": Numeric: lengths (3808, 0) differ
     Component "affiliation_pos": Numeric: lengths (3808, 0) differ
     Component "source": Lengths (3808, 0) differ (string compare on first 0)
     Component "identifier": Lengths (3808, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10032, 18) differ >
     Component "pmid": Numeric: lengths (10032, 18) differ
     Component "author_pos": Numeric: lengths (10032, 18) differ
     Component "source": Lengths (10032, 18) differ (string compare on first 18)
     Component "identifier": Lengths (10032, 18) differ (string compare on first 18)
     Component "identifier": 18 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     author_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10580, 28) differ >
     Component "pmid": Numeric: lengths (10580, 28) differ
     Component "complete": Lengths (10580, 28) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     chemical not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2075, 0) differ >
     Component "pmid": Numeric: lengths (2075, 0) differ
     Component "registry_number": Lengths (2075, 0) differ (string compare on first 0)
     Component "substance_name": Lengths (2075, 0) differ (string compare on first 0)
     Component "substance_ui": Lengths (2075, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     comment not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (250, 3) differ >
     Component "pmid": Numeric: lengths (250, 3) differ
     Component "ref_type": Lengths (250, 3) differ (string compare on first 3)
     Component "ref_type": 3 string mismatches
     Component "ref_pmid": Numeric: lengths (250, 3) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     data_bank not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (214, 4) differ >
     Component "pmid": Numeric: lengths (214, 4) differ
     Component "data_bank_name": Lengths (214, 4) differ (string compare on first 4)
     Component "data_bank_name": 3 string mismatches
     Component "accession_number": Lengths (214, 4) differ (string compare on first 4)
     Component "accession_number": 4 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     grant_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2770, 16) differ >
     Component "pmid": Numeric: lengths (2770, 16) differ
     Component "grant_id": Lengths (2770, 16) differ (string compare on first 16)
     Component "grant_id": 'is.NA' value mismatch: 0 in current 5 in target
     Component "acronym": Lengths (2770, 16) differ (string compare on first 16)
     Component "acronym": 'is.NA' value mismatch: 13 in current 16 in target
     Component "agency": Lengths (2770, 16) differ (string compare on first 16)
     Component "agency": 16 string mismatches
     Component "country": Lengths (2770, 16) differ (string compare on first 16)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     grant_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1042, 6) differ >
     Component "pmid": Numeric: lengths (1042, 6) differ
     Component "complete": Lengths (1042, 6) differ (string compare on first 6)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     investigator not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1434, 27) differ >
     Component "pmid": Numeric: lengths (1434, 27) differ
     Component "investigator_pos": Numeric: lengths (1434, 27) differ
     Component "last_name": Lengths (1434, 27) differ (string compare on first 27)
     Component "last_name": 27 string mismatches
     Component "fore_name": Lengths (1434, 27) differ (string compare on first 27)
     Component "fore_name": 27 string mismatches
     Component "initials": Lengths (1434, 27) differ (string compare on first 27)
     Component "initials": 26 string mismatches
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (73, 0) differ >
     Component "pmid": Numeric: lengths (73, 0) differ
     Component "investigator_pos": Numeric: lengths (73, 0) differ
     Component "affiliation_pos": Numeric: lengths (73, 0) differ
     Component "affiliation": Lengths (73, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     journal not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "journal_name": Lengths (10710, 28) differ (string compare on first 28)
     Component "journal_name": 28 string mismatches
     Component "journal_iso": Lengths (10710, 28) differ (string compare on first 28)
     Component "journal_iso": 28 string mismatches
     Component "pub_date": Numeric: lengths (10710, 28) differ
     Component "pub_year": Lengths (10710, 28) differ (string compare on first 28)
     Component "pub_year": 28 string mismatches
     ...
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     keyword_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (41142, 102) differ >
     Component "pmid": Numeric: lengths (41142, 102) differ
     Component "keyword_name": Lengths (41142, 102) differ (string compare on first 102)
     Component "keyword_name": 102 string mismatches
     Component "major_topic": Lengths (41142, 102) differ (string compare on first 102)
     Component "major_topic": 6 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     keyword_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (7781, 20) differ >
     Component "pmid": Numeric: lengths (7781, 20) differ
     Component "list_owner": Lengths (7781, 20) differ (string compare on first 20)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (11553, 0) differ >
     Component "pmid": Numeric: lengths (11553, 0) differ
     Component "descriptor_pos": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_name": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_ui": Lengths (11553, 0) differ (string compare on first 0)
     Component "descriptor_major_topic": Lengths (11553, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (1659, 0) differ >
     Component "pmid": Numeric: lengths (1659, 0) differ
     Component "indexing_method": Lengths (1659, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3968, 0) differ >
     Component "pmid": Numeric: lengths (3968, 0) differ
     Component "descriptor_pos": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_name": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_ui": Lengths (3968, 0) differ (string compare on first 0)
     Component "qualifier_major_topic": Lengths (3968, 0) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     other_abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (216, 2) differ >
     Component "pmid": Numeric: lengths (216, 2) differ
     Component "text": Lengths (216, 2) differ (string compare on first 2)
     Component "text": 2 string mismatches
     Component "type": Lengths (216, 2) differ (string compare on first 2)
     Component "type": 1 string mismatch
     Component "language": Lengths (216, 2) differ (string compare on first 2)
     Component "language": 2 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pmid_status not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (10710, 28) differ >
     Component "pmid": Numeric: lengths (10710, 28) differ
     Component "version": Numeric: lengths (10710, 28) differ
     Component "xml_filename": Lengths (10710, 28) differ (string compare on first 28)
     Component "xml_filename": 28 string mismatches
     Component "status": Lengths (10710, 28) differ (string compare on first 28)
     Component "status": 15 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pub_history not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (50281, 127) differ >
     Component "pmid": Numeric: lengths (50281, 127) differ
     Component "pub_status": Lengths (50281, 127) differ (string compare on first 127)
     Component "pub_status": 91 string mismatches
     Component "pub_date": Numeric: lengths (50281, 127) differ
     ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
     pub_type not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (12429, 30) differ >
     Component "pmid": Numeric: lengths (12429, 30) differ
     Component "type_name": Lengths (12429, 30) differ (string compare on first 30)
     Component "type_name": 13 string mismatches
     Component "type_id": Lengths (12429, 30) differ (string compare on first 30)
     Component "type_id": 13 string mismatches
     ── Failure ('test_modify_pubmed_db_std.R:32'): 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'): modifyPubmedDb update matches standard ──
     abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (57, 117) differ >
     Component "pmid": Numeric: lengths (57, 117) differ
     Component "text": Lengths (57, 117) differ (string compare on first 57)
     Component "label": Lengths (57, 117) differ (string compare on first 57)
     Component "nlm_category": Lengths (57, 117) differ (string compare on first 57)
     Component "abstract_pos": Numeric: lengths (57, 117) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (19, 34) differ >
     Component "pmid": Numeric: lengths (19, 34) differ
     Component "copyright": Lengths (19, 34) differ (string compare on first 19)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     article not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "title": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_date": Numeric: lengths (28, 58) differ
     Component "pub_model": Lengths (28, 58) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     article_id not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (38, 76) differ >
     Component "pmid": Numeric: lengths (38, 76) differ
     Component "id_type": Lengths (38, 76) differ (string compare on first 38)
     Component "id_value": Lengths (38, 76) differ (string compare on first 38)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (197, 386) differ >
     Component "pmid": Numeric: lengths (197, 386) differ
     Component "author_pos": Numeric: lengths (197, 386) differ
     Component "last_name": Lengths (197, 386) differ (string compare on first 197)
     Component "fore_name": Lengths (197, 386) differ (string compare on first 197)
     Component "initials": Lengths (197, 386) differ (string compare on first 197)
     Component "suffix": Lengths (197, 386) differ (string compare on first 197)
     Component "valid": Lengths (197, 386) differ (string compare on first 197)
     Component "equal_contrib": Lengths (197, 386) differ (string compare on first 197)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (218, 453) differ >
     Component "pmid": Numeric: lengths (218, 453) differ
     Component "author_pos": Numeric: lengths (218, 453) differ
     Component "affiliation_pos": Numeric: lengths (218, 453) differ
     Component "affiliation": Lengths (218, 453) differ (string compare on first 218)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_identifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (18, 60) differ >
     Component "pmid": Numeric: lengths (18, 60) differ
     Component "author_pos": Numeric: lengths (18, 60) differ
     Component "source": Lengths (18, 60) differ (string compare on first 18)
     Component "identifier": Lengths (18, 60) differ (string compare on first 18)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     author_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "complete": Lengths (28, 58) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     chemical not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 44) differ >
     Component "pmid": Numeric: lengths (0, 44) differ
     Component "registry_number": Lengths (0, 44) differ (string compare on first 0)
     Component "substance_name": Lengths (0, 44) differ (string compare on first 0)
     Component "substance_ui": Lengths (0, 44) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     comment not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (3, 8) differ >
     Component "pmid": Numeric: lengths (3, 8) differ
     Component "ref_type": Lengths (3, 8) differ (string compare on first 3)
     Component "ref_pmid": Numeric: lengths (3, 8) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     data_bank not equal to DBI::dbReadTable(conExp, tableName).
     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'): modifyPubmedDb update matches standard ──
     grant_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (16, 34) differ >
     Component "pmid": Numeric: lengths (16, 34) differ
     Component "grant_id": Lengths (16, 34) differ (string compare on first 16)
     Component "acronym": Lengths (16, 34) differ (string compare on first 16)
     Component "agency": Lengths (16, 34) differ (string compare on first 16)
     Component "country": Lengths (16, 34) differ (string compare on first 16)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     grant_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (6, 12) differ >
     Component "pmid": Numeric: lengths (6, 12) differ
     Component "complete": Lengths (6, 12) differ (string compare on first 6)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     investigator not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (27, 54) differ >
     Component "pmid": Numeric: lengths (27, 54) differ
     Component "investigator_pos": Numeric: lengths (27, 54) differ
     Component "last_name": Lengths (27, 54) differ (string compare on first 27)
     Component "fore_name": Lengths (27, 54) differ (string compare on first 27)
     Component "initials": Lengths (27, 54) differ (string compare on first 27)
     Component "suffix": Lengths (27, 54) differ (string compare on first 27)
     Component "valid": Lengths (27, 54) differ (string compare on first 27)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     journal not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 58) differ >
     Component "pmid": Numeric: lengths (28, 58) differ
     Component "journal_name": Lengths (28, 58) differ (string compare on first 28)
     Component "journal_iso": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_date": Numeric: lengths (28, 58) differ
     Component "pub_year": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_month": Lengths (28, 58) differ (string compare on first 28)
     Component "pub_day": Lengths (28, 58) differ (string compare on first 28)
     Component "medline_date": Lengths (28, 58) differ (string compare on first 28)
     ...
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     keyword_item not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (102, 195) differ >
     Component "pmid": Numeric: lengths (102, 195) differ
     Component "keyword_name": Lengths (102, 195) differ (string compare on first 102)
     Component "major_topic": Lengths (102, 195) differ (string compare on first 102)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     keyword_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (20, 39) differ >
     Component "pmid": Numeric: lengths (20, 39) differ
     Component "list_owner": Lengths (20, 39) differ (string compare on first 20)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 256) differ >
     Component "pmid": Numeric: lengths (0, 256) differ
     Component "descriptor_pos": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_name": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_ui": Lengths (0, 256) differ (string compare on first 0)
     Component "descriptor_major_topic": Lengths (0, 256) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_list not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 13) differ >
     Component "pmid": Numeric: lengths (0, 13) differ
     Component "indexing_method": Lengths (0, 13) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (0, 152) differ >
     Component "pmid": Numeric: lengths (0, 152) differ
     Component "descriptor_pos": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_name": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_ui": Lengths (0, 152) differ (string compare on first 0)
     Component "qualifier_major_topic": Lengths (0, 152) differ (string compare on first 0)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     other_abstract not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (2, 4) differ >
     Component "pmid": Numeric: lengths (2, 4) differ
     Component "text": Lengths (2, 4) differ (string compare on first 2)
     Component "type": Lengths (2, 4) differ (string compare on first 2)
     Component "language": Lengths (2, 4) differ (string compare on first 2)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pmid_status not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (28, 106) differ >
     Component "pmid": Numeric: lengths (28, 106) differ
     Component "version": Numeric: lengths (28, 106) differ
     Component "xml_filename": Lengths (28, 106) differ (string compare on first 28)
     Component "status": Lengths (28, 106) differ (string compare on first 28)
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pub_history not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (127, 254) differ >
     Component "pmid": Numeric: lengths (127, 254) differ
     Component "pub_status": Lengths (127, 254) differ (string compare on first 127)
     Component "pub_date": Numeric: lengths (127, 254) differ
     ── Failure ('test_modify_pubmed_db_std.R:52'): modifyPubmedDb update matches standard ──
     pub_type not equal to DBI::dbReadTable(conExp, tableName).
     Attributes: < Component "row.names": Numeric: lengths (30, 79) differ >
     Component "pmid": Numeric: lengths (30, 79) differ
     Component "type_name": Lengths (30, 79) differ (string compare on first 30)
     Component "type_id": Lengths (30, 79) differ (string compare on first 30)
    
     [ FAIL 51 | WARN 0 | SKIP 4 | PASS 136 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.13
Check: tests
Result: ERROR
     Running 'testthat.R' [22s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(pmparser)
     >
     > test_check('pmparser')
     [ FAIL 2 | WARN 4 | SKIP 4 | PASS 127 ]
    
     == Skipped tests ===============================================================
     * On CRAN (4)
    
     == Failed tests ================================================================
     -- Error ('test_modify_pubmed_db_dup.R:51'): modifyPubmedDb create is unique ---
     Error in `gzfile(file, open = "rb")`: cannot open the connection
     Backtrace:
     x
     1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:2
     2. \-pmparser::getCitation(...)
     3. \-pmparser:::writeTableInChunks(...)
     4. +-R.utils::countLines(path)
     5. \-R.utils::countLines.default(path)
     6. \-base::gzfile(file, open = "rb")
     -- Error ('test_modify_pubmed_db_std.R:22'): modifyPubmedDb create matches standard --
     Error in `gzfile(file, open = "rb")`: cannot open the connection
     Backtrace:
     x
     1. \-pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:2
     2. \-pmparser::getCitation(...)
     3. \-pmparser:::writeTableInChunks(...)
     4. +-R.utils::countLines(path)
     5. \-R.utils::countLines.default(path)
     6. \-base::gzfile(file, open = "rb")
    
     [ FAIL 2 | WARN 4 | SKIP 4 | PASS 127 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64