• using R Under development (unstable) (2026-01-31 r89365)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘pmparser/DESCRIPTION’ ... OK
• this is package ‘pmparser’ version ‘1.0.23’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘pmparser’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [13s/14s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [16m/17m] ERROR   Running ‘testthat.R’ [16m/17m] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(pmparser)   >   > test_check('pmparser')   trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5'   Content type 'application/x-gzip' length 60 bytes   ==================================================   downloaded 60 bytes      trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz'   Content type 'application/x-gzip' length 13837691 bytes (13.2 MB)   ==================================================   downloaded 13.2 MB      trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5'   Content type 'application/x-gzip' length 60 bytes   ==================================================   downloaded 60 bytes      trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz'   Content type 'application/x-gzip' length 44629574 bytes (42.6 MB)   ==================================================   downloaded 42.6 MB      Saving _problems/test_modify_pubmed_db_dup-76.R   Saving _problems/test_modify_pubmed_db_dup-76.R   trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5'   Content type 'application/x-gzip' length 60 bytes   ==================================================   downloaded 60 bytes      trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz'   Content type 'application/x-gzip' length 13837691 bytes (13.2 MB)   ==================================================   downloaded 13.2 MB      Saving _problems/test_modify_pubmed_db_std-34.R   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   trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5'   Content type 'application/x-gzip' length 60 bytes   ==================================================   downloaded 60 bytes      trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz'   Content type 'application/x-gzip' length 44629574 bytes (42.6 MB)   ==================================================   downloaded 42.6 MB      Saving _problems/test_modify_pubmed_db_std-54.R   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   Saving _problems/test_modify_pubmed_db_std-54.R   Saving _problems/test_modify_pubmed_db_std-54.R   [ FAIL 56 | WARN 4 | SKIP 4 | PASS 131 ]      ══ Skipped tests (4) ═══════════════════════════════════════════════════════════   • On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3',     'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique ──   Expected data_bank to equal 0L.   Differences:   1/1 mismatches   [1] 101 - 0 == 101   ── Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique ──   Expected mesh_qualifier to equal 0L.   Differences:   1/1 mismatches   [1] 405 - 0 == 405   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected abstract to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (9603, 68) differ >   Component "pmid": Numeric: lengths (9603, 68) differ   Component "text": Lengths (9603, 68) differ (string compare on first 68)   Component "text": 68 string mismatches   Component "label": Lengths (9603, 68) differ (string compare on first 68)   Component "label": 'is.NA' value mismatch: 15 in current 13 in target   Component "nlm_category": Lengths (9603, 68) differ (string compare on first 68)   Component "nlm_category": 'is.NA' value mismatch: 15 in current 13 in target   Component "abstract_pos": Numeric: lengths (9603, 68) differ   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected abstract_copyright to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (3219, 22) differ >   Component "pmid": Numeric: lengths (3219, 22) differ   Component "copyright": Lengths (3219, 22) differ (string compare on first 22)   Component "copyright": 22 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected article to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >   Component "pmid": Numeric: lengths (4989, 30) differ   Component "title": Lengths (4989, 30) differ (string compare on first 30)   Component "title": 30 string mismatches   Component "language": Lengths (4989, 30) differ (string compare on first 30)   Component "language": 2 string mismatches   Component "vernacular_title": Lengths (4989, 30) differ (string compare on first 30)   Component "vernacular_title": 'is.NA' value mismatch: 28 in current 30 in target   Component "pub_model": Lengths (4989, 30) differ (string compare on first 30)   ...   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected article_id to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (6359, 40) differ >   Component "pmid": Numeric: lengths (6359, 40) differ   Component "id_type": Lengths (6359, 40) differ (string compare on first 40)   Component "id_type": 10 string mismatches   Component "id_value": Lengths (6359, 40) differ (string compare on first 40)   Component "id_value": 40 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected author to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (34978, 279) differ >   Component "pmid": Numeric: lengths (34978, 279) differ   Component "author_pos": Numeric: lengths (34978, 279) differ   Component "last_name": Lengths (34978, 279) differ (string compare on first 279)   Component "last_name": 'is.NA' value mismatch: 4 in current 0 in target   Component "fore_name": Lengths (34978, 279) differ (string compare on first 279)   Component "fore_name": 'is.NA' value mismatch: 5 in current 0 in target   Component "initials": Lengths (34978, 279) differ (string compare on first 279)   Component "initials": 'is.NA' value mismatch: 5 in current 0 in target   ...   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected author_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (42448, 337) differ >   Component "pmid": Numeric: lengths (42448, 337) differ   Component "author_pos": Numeric: lengths (42448, 337) differ   Component "affiliation_pos": Numeric: lengths (42448, 337) differ   Component "affiliation": Lengths (42448, 337) differ (string compare on first 337)   Component "affiliation": 337 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected author_affiliation_identifier to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (989, 0) differ >   Component "pmid": Numeric: lengths (989, 0) differ   Component "author_pos": Numeric: lengths (989, 0) differ   Component "affiliation_pos": Numeric: lengths (989, 0) differ   Component "source": Lengths (989, 0) differ (string compare on first 0)   Component "identifier": Lengths (989, 0) differ (string compare on first 0)   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected author_identifier to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (7607, 29) differ >   Component "pmid": Numeric: lengths (7607, 29) differ   Component "author_pos": Numeric: lengths (7607, 29) differ   Component "source": Lengths (7607, 29) differ (string compare on first 29)   Component "identifier": Lengths (7607, 29) differ (string compare on first 29)   Component "identifier": 29 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected author_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (4932, 30) differ >   Component "pmid": Numeric: lengths (4932, 30) differ   Component "complete": Lengths (4932, 30) differ (string compare on first 30)   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected chemical to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (1777, 5) differ >   Component "pmid": Numeric: lengths (1777, 5) differ   Component "registry_number": Lengths (1777, 5) differ (string compare on first 5)   Component "registry_number": 3 string mismatches   Component "substance_name": Lengths (1777, 5) differ (string compare on first 5)   Component "substance_name": 5 string mismatches   Component "substance_ui": Lengths (1777, 5) differ (string compare on first 5)   Component "substance_ui": 5 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected comment to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (150, 3) differ >   Component "pmid": Numeric: lengths (150, 3) differ   Component "ref_type": Lengths (150, 3) differ (string compare on first 3)   Component "ref_type": 1 string mismatch   Component "ref_pmid": Numeric: lengths (150, 3) differ   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected data_bank to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (70, 4) differ >   Component "pmid": Numeric: lengths (70, 4) differ   Component "data_bank_name": Lengths (70, 4) differ (string compare on first 4)   Component "accession_number": Lengths (70, 4) differ (string compare on first 4)   Component "accession_number": 4 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected grant_item to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (2637, 35) differ >   Component "pmid": Numeric: lengths (2637, 35) differ   Component "grant_id": Lengths (2637, 35) differ (string compare on first 35)   Component "grant_id": 'is.NA' value mismatch: 6 in current 8 in target   Component "acronym": Lengths (2637, 35) differ (string compare on first 35)   Component "acronym": 'is.NA' value mismatch: 20 in current 34 in target   Component "agency": Lengths (2637, 35) differ (string compare on first 35)   Component "agency": 35 string mismatches   Component "country": Lengths (2637, 35) differ (string compare on first 35)   ...   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected grant_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (909, 8) differ >   Component "pmid": Numeric: lengths (909, 8) differ   Component "complete": Lengths (909, 8) differ (string compare on first 8)   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected investigator to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (2074, 80) differ >   Component "pmid": Numeric: lengths (2074, 80) differ   Component "investigator_pos": Numeric: lengths (2074, 80) differ   Component "last_name": Lengths (2074, 80) differ (string compare on first 80)   Component "last_name": 80 string mismatches   Component "fore_name": Lengths (2074, 80) differ (string compare on first 80)   Component "fore_name": 80 string mismatches   Component "initials": Lengths (2074, 80) differ (string compare on first 80)   Component "initials": 73 string mismatches   ...   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected investigator_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (45, 53) differ >   Component "pmid": Numeric: lengths (45, 53) differ   Component "investigator_pos": Numeric: lengths (45, 53) differ   Component "affiliation_pos": Numeric: lengths (45, 53) differ   Component "affiliation": Lengths (45, 53) differ (string compare on first 45)   Component "affiliation": 45 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected journal to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >   Component "pmid": Numeric: lengths (4989, 30) differ   Component "journal_name": Lengths (4989, 30) differ (string compare on first 30)   Component "journal_name": 30 string mismatches   Component "journal_iso": Lengths (4989, 30) differ (string compare on first 30)   Component "journal_iso": 30 string mismatches   Component "pub_date": Numeric: lengths (4989, 30) differ   Component "pub_year": Lengths (4989, 30) differ (string compare on first 30)   Component "pub_year": 30 string mismatches   ...   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected keyword_item to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (19167, 109) differ >   Component "pmid": Numeric: lengths (19167, 109) differ   Component "keyword_name": Lengths (19167, 109) differ (string compare on first 109)   Component "keyword_name": 109 string mismatches   Component "major_topic": Lengths (19167, 109) differ (string compare on first 109)   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected keyword_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (3596, 21) differ >   Component "pmid": Numeric: lengths (3596, 21) differ   Component "list_owner": Lengths (3596, 21) differ (string compare on first 21)   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected mesh_descriptor to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (11460, 74) differ >   Component "pmid": Numeric: lengths (11460, 74) differ   Component "descriptor_pos": Lengths (11460, 74) differ (string compare on first 74)   Component "descriptor_pos": 65 string mismatches   Component "descriptor_name": Lengths (11460, 74) differ (string compare on first 74)   Component "descriptor_name": 71 string mismatches   Component "descriptor_ui": Lengths (11460, 74) differ (string compare on first 74)   Component "descriptor_ui": 71 string mismatches   Component "descriptor_major_topic": Lengths (11460, 74) differ (string compare on first 74)   ...   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected mesh_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >   Component "pmid": Numeric: lengths (4989, 30) differ   Component "indexing_method": Lengths (4989, 30) differ (string compare on first 30)   Component "indexing_method": 1 string mismatch   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected mesh_qualifier to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (7130, 39) differ >   Component "pmid": Numeric: lengths (7130, 39) differ   Component "descriptor_pos": Lengths (7130, 39) differ (string compare on first 39)   Component "descriptor_pos": 35 string mismatches   Component "qualifier_name": Lengths (7130, 39) differ (string compare on first 39)   Component "qualifier_name": 38 string mismatches   Component "qualifier_ui": Lengths (7130, 39) differ (string compare on first 39)   Component "qualifier_ui": 38 string mismatches   Component "qualifier_major_topic": Lengths (7130, 39) differ (string compare on first 39)   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected other_abstract to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (147, 4) differ >   Component "pmid": Numeric: lengths (147, 4) differ   Component "text": Lengths (147, 4) differ (string compare on first 4)   Component "text": 4 string mismatches   Component "type": Lengths (147, 4) differ (string compare on first 4)   Component "type": 2 string mismatches   Component "language": Lengths (147, 4) differ (string compare on first 4)   Component "language": 4 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected pmid_status to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ >   Component "pmid": Numeric: lengths (4989, 30) differ   Component "version": Numeric: lengths (4989, 30) differ   Component "xml_filename": Lengths (4989, 30) differ (string compare on first 30)   Component "xml_filename": 30 string mismatches   Component "status": Lengths (4989, 30) differ (string compare on first 30)   Component "status": 14 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected pub_history to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (22724, 143) differ >   Component "pmid": Numeric: lengths (22724, 143) differ   Component "pub_status": Lengths (22724, 143) differ (string compare on first 143)   Component "pub_status": 100 string mismatches   Component "pub_date": Numeric: lengths (22724, 143) differ   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected pub_type to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (6060, 37) differ >   Component "pmid": Numeric: lengths (6060, 37) differ   Component "type_name": Lengths (6060, 37) differ (string compare on first 37)   Component "type_name": 12 string mismatches   Component "type_id": Lengths (6060, 37) differ (string compare on first 37)   Component "type_id": 12 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──   Expected readme to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Component "text": 1 string mismatch   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected abstract to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (27961, 126) differ >   Component "pmid": Numeric: lengths (27961, 126) differ   Component "text": Lengths (27961, 126) differ (string compare on first 126)   Component "text": 58 string mismatches   Component "label": Lengths (27961, 126) differ (string compare on first 126)   Component "label": 'is.NA' value mismatch: 34 in current 27 in target   Component "nlm_category": Lengths (27961, 126) differ (string compare on first 126)   Component "nlm_category": 'is.NA' value mismatch: 34 in current 50 in target   Component "abstract_pos": Numeric: lengths (27961, 126) differ   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected abstract_copyright to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (9124, 43) differ >   Component "pmid": Numeric: lengths (9124, 43) differ   Component "copyright": Lengths (9124, 43) differ (string compare on first 43)   Component "copyright": 21 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected article to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ >   Component "pmid": Numeric: lengths (14308, 60) differ   Component "title": Lengths (14308, 60) differ (string compare on first 60)   Component "title": 30 string mismatches   Component "language": Lengths (14308, 60) differ (string compare on first 60)   Component "vernacular_title": Lengths (14308, 60) differ (string compare on first 60)   Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target   Component "pub_model": Lengths (14308, 60) differ (string compare on first 60)   Component "pub_model": 19 string mismatches   ...   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected article_id to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (16828, 76) differ >   Component "pmid": Numeric: lengths (16828, 76) differ   Component "id_type": Lengths (16828, 76) differ (string compare on first 76)   Component "id_type": 10 string mismatches   Component "id_value": Lengths (16828, 76) differ (string compare on first 76)   Component "id_value": 36 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected author to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (101991, 490) differ >   Component "pmid": Numeric: lengths (101991, 490) differ   Component "author_pos": Numeric: lengths (101991, 490) differ   Component "last_name": Lengths (101991, 490) differ (string compare on first 490)   Component "last_name": 'is.NA' value mismatch: 6 in current 4 in target   Component "fore_name": Lengths (101991, 490) differ (string compare on first 490)   Component "fore_name": 'is.NA' value mismatch: 7 in current 5 in target   Component "initials": Lengths (101991, 490) differ (string compare on first 490)   Component "initials": 'is.NA' value mismatch: 7 in current 5 in target   ...   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected author_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (121076, 614) differ >   Component "pmid": Numeric: lengths (121076, 614) differ   Component "author_pos": Numeric: lengths (121076, 614) differ   Component "affiliation_pos": Numeric: lengths (121076, 614) differ   Component "affiliation": Lengths (121076, 614) differ (string compare on first 614)   Component "affiliation": 277 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected author_affiliation_identifier to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (3559, 0) differ >   Component "pmid": Numeric: lengths (3559, 0) differ   Component "author_pos": Numeric: lengths (3559, 0) differ   Component "affiliation_pos": Numeric: lengths (3559, 0) differ   Component "source": Lengths (3559, 0) differ (string compare on first 0)   Component "identifier": Lengths (3559, 0) differ (string compare on first 0)   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected author_identifier to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (21074, 61) differ >   Component "pmid": Numeric: lengths (21074, 61) differ   Component "author_pos": Numeric: lengths (21074, 61) differ   Component "source": Lengths (21074, 61) differ (string compare on first 61)   Component "identifier": Lengths (21074, 61) differ (string compare on first 61)   Component "identifier": 32 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected author_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (14209, 59) differ >   Component "pmid": Numeric: lengths (14209, 59) differ   Component "complete": Lengths (14209, 59) differ (string compare on first 59)   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected chemical to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (9674, 16) differ >   Component "pmid": Numeric: lengths (9674, 16) differ   Component "registry_number": Lengths (9674, 16) differ (string compare on first 16)   Component "registry_number": 8 string mismatches   Component "substance_name": Lengths (9674, 16) differ (string compare on first 16)   Component "substance_name": 11 string mismatches   Component "substance_ui": Lengths (9674, 16) differ (string compare on first 16)   Component "substance_ui": 11 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected comment to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (898, 6) differ >   Component "pmid": Numeric: lengths (898, 6) differ   Component "ref_type": Lengths (898, 6) differ (string compare on first 6)   Component "ref_type": 3 string mismatches   Component "ref_pmid": Numeric: lengths (898, 6) differ   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected data_bank to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (267, 6) differ >   Component "pmid": Numeric: lengths (267, 6) differ   Component "data_bank_name": Lengths (267, 6) differ (string compare on first 6)   Component "data_bank_name": 1 string mismatch   Component "accession_number": Lengths (267, 6) differ (string compare on first 6)   Component "accession_number": 2 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected grant_item to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (8770, 57) differ >   Component "pmid": Numeric: lengths (8770, 57) differ   Component "grant_id": Lengths (8770, 57) differ (string compare on first 57)   Component "grant_id": 'is.NA' value mismatch: 13 in current 8 in target   Component "acronym": Lengths (8770, 57) differ (string compare on first 57)   Component "acronym": 'is.NA' value mismatch: 42 in current 22 in target   Component "agency": Lengths (8770, 57) differ (string compare on first 57)   Component "agency": 22 string mismatches   Component "country": Lengths (8770, 57) differ (string compare on first 57)   ...   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected grant_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (3033, 17) differ >   Component "pmid": Numeric: lengths (3033, 17) differ   Component "complete": Lengths (3033, 17) differ (string compare on first 17)   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected investigator to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (5842, 144) differ >   Component "pmid": Numeric: lengths (5842, 144) differ   Component "investigator_pos": Numeric: lengths (5842, 144) differ   Component "last_name": Lengths (5842, 144) differ (string compare on first 144)   Component "last_name": 64 string mismatches   Component "fore_name": Lengths (5842, 144) differ (string compare on first 144)   Component "fore_name": 64 string mismatches   Component "initials": Lengths (5842, 144) differ (string compare on first 144)   Component "initials": 59 string mismatches   ...   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected investigator_affiliation to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (227, 53) differ >   Component "pmid": Numeric: lengths (227, 53) differ   Component "investigator_pos": Numeric: lengths (227, 53) differ   Component "affiliation_pos": Numeric: lengths (227, 53) differ   Component "affiliation": Lengths (227, 53) differ (string compare on first 53)   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected investigator_identifier to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (2, 0) differ >   Component "pmid": Numeric: lengths (2, 0) differ   Component "investigator_pos": Numeric: lengths (2, 0) differ   Component "source": Lengths (2, 0) differ (string compare on first 0)   Component "identifier": Lengths (2, 0) differ (string compare on first 0)   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected journal to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ >   Component "pmid": Numeric: lengths (14308, 60) differ   Component "journal_name": Lengths (14308, 60) differ (string compare on first 60)   Component "journal_name": 30 string mismatches   Component "journal_iso": Lengths (14308, 60) differ (string compare on first 60)   Component "journal_iso": 30 string mismatches   Component "pub_date": Numeric: lengths (14308, 60) differ   Component "pub_year": Lengths (14308, 60) differ (string compare on first 60)   Component "pub_year": 30 string mismatches   ...   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected keyword_item to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (57226, 229) differ >   Component "pmid": Numeric: lengths (57226, 229) differ   Component "keyword_name": Lengths (57226, 229) differ (string compare on first 229)   Component "keyword_name": 120 string mismatches   Component "major_topic": Lengths (57226, 229) differ (string compare on first 229)   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected keyword_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (10762, 43) differ >   Component "pmid": Numeric: lengths (10762, 43) differ   Component "list_owner": Lengths (10762, 43) differ (string compare on first 43)   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected mesh_descriptor to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (72995, 140) differ >   Component "pmid": Numeric: lengths (72995, 140) differ   Component "descriptor_pos": Lengths (72995, 140) differ (string compare on first 140)   Component "descriptor_pos": 51 string mismatches   Component "descriptor_name": Lengths (72995, 140) differ (string compare on first 140)   Component "descriptor_name": 66 string mismatches   Component "descriptor_ui": Lengths (72995, 140) differ (string compare on first 140)   Component "descriptor_ui": 66 string mismatches   Component "descriptor_major_topic": Lengths (72995, 140) differ (string compare on first 140)   ...   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected mesh_list to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (6973, 36) differ >   Component "pmid": Numeric: lengths (6973, 36) differ   Component "indexing_method": Lengths (6973, 36) differ (string compare on first 36)   Component "indexing_method": 6 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected mesh_qualifier to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (42278, 88) differ >   Component "pmid": Numeric: lengths (42278, 88) differ   Component "descriptor_pos": Lengths (42278, 88) differ (string compare on first 88)   Component "descriptor_pos": 49 string mismatches   Component "qualifier_name": Lengths (42278, 88) differ (string compare on first 88)   Component "qualifier_name": 47 string mismatches   Component "qualifier_ui": Lengths (42278, 88) differ (string compare on first 88)   Component "qualifier_ui": 47 string mismatches   Component "qualifier_major_topic": Lengths (42278, 88) differ (string compare on first 88)   ...   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected other_abstract to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (417, 7) differ >   Component "pmid": Numeric: lengths (417, 7) differ   Component "text": Lengths (417, 7) differ (string compare on first 7)   Component "text": 3 string mismatches   Component "type": Lengths (417, 7) differ (string compare on first 7)   Component "type": 2 string mismatches   Component "language": Lengths (417, 7) differ (string compare on first 7)   Component "language": 3 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected pmid_status to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (14327, 60) differ >   Component "pmid": Numeric: lengths (14327, 60) differ   Component "version": Numeric: lengths (14327, 60) differ   Component "xml_filename": Lengths (14327, 60) differ (string compare on first 60)   Component "xml_filename": 30 string mismatches   Component "status": Lengths (14327, 60) differ (string compare on first 60)   Component "status": 24 string mismatches   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected pub_history to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (70114, 293) differ >   Component "pmid": Numeric: lengths (70114, 293) differ   Component "pub_status": Lengths (70114, 293) differ (string compare on first 293)   Component "pub_status": 114 string mismatches   Component "pub_date": Numeric: lengths (70114, 293) differ   ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──   Expected pub_type to equal `DBI::dbReadTable(conExp, tableName)`.   Differences:   Attributes: < Component "row.names": Numeric: lengths (19407, 74) differ >   Component "pmid": Numeric: lengths (19407, 74) differ   Component "type_name": Lengths (19407, 74) differ (string compare on first 74)   Component "type_name": 27 string mismatches   Component "type_id": Lengths (19407, 74) differ (string compare on first 74)   Component "type_id": 27 string mismatches      [ FAIL 56 | WARN 4 | SKIP 4 | PASS 131 ]   Error:   ! Test failures.   Warning message:   call dbDisconnect() when finished working with a connection   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [17s/17s] OK
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR