CRAN Package Check Results for Package pmparser

Last updated on 2025-12-28 01:48:47 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0.23	4.99	55.67	60.66	OK
r-devel-linux-x86_64-debian-gcc	1.0.23	2.92	38.89	41.81	OK
r-devel-linux-x86_64-fedora-clang	1.0.23	9.00	85.67	94.67	OK
r-devel-linux-x86_64-fedora-gcc	1.0.23	8.00	108.55	116.55	OK
r-devel-windows-x86_64	1.0.23	6.00	75.00	81.00	ERROR
r-patched-linux-x86_64	1.0.23	4.71	49.74	54.45	OK
r-release-linux-x86_64	1.0.23	4.03	49.93	53.96	OK
r-release-macos-arm64	1.0.23	1.00	51.00	52.00	OK
r-release-macos-x86_64	1.0.23	4.00	103.00	107.00	OK
r-release-windows-x86_64	1.0.23	7.00	73.00	80.00	OK
r-oldrel-macos-arm64	1.0.23	1.00	49.00	50.00	OK
r-oldrel-macos-x86_64	1.0.23	4.00	136.00	140.00	OK
r-oldrel-windows-x86_64	1.0.23	8.00	87.00	95.00	OK

Check Details

Version: 1.0.23
Check: examples
Result: ERROR Running examples in 'pmparser-Ex.R' failed The error most likely occurred in: > ### Name: parseElement > ### Title: Parse elements from a PubMed XML file > ### Aliases: parseElement parsePmidStatus parseArticleId parseArticle > ### parsePubHistory parseJournal parsePubType parseMesh parseKeyword > ### parseGrant parseChemical parseDataBank parseComment parseAbstract > ### parseOther parseAuthor parseInvestigator > > ### ** Examples > > library('data.table') Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > library('xml2') > > filename = 'pubmed20n1016.xml.gz' > rawXml = read_xml(system.file('extdata', filename, package = 'pmparser')) > > pmidStatusList = parsePmidStatus(rawXml, filename) > pmXml = pmidStatusList[[1L]] > dPmidRaw = pmidStatusList[[2L]] > dPmid = dPmidRaw[status != 'Deleted', !'status'] > > dArticleId = parseArticleId(pmXml, dPmid) > dArticle = parseArticle(pmXml, dPmid) > dJournal = parseJournal(pmXml, dPmid) > dPubType = parsePubType(pmXml, dPmid) > dPubHistory = parsePubHistory(pmXml, dPmid) > meshRes = parseMesh(pmXml, dPmid) Error in `[.data.table`(x3, , `:=`(descriptor_pos, seq_len(.N)), by = pmid) : attempt access index 6/6 in VECTOR_ELT Calls: parseMesh -> [ -> [.data.table Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.23
Check: tests
Result: ERROR Running 'testthat.R' [20s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(pmparser) > > test_check('pmparser') Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-34.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_modify_pubmed_db_std-54.R Saving _problems/test_parse_element-46.R Saving _problems/test_parse_element-76.R Saving _problems/test_parse_element-81.R Saving _problems/test_parse_element-86.R [ FAIL 25 | WARN 0 | SKIP 4 | PASS 162 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3', 'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected abstract to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 68) differ > Component "pmid": Numeric: lengths (0, 68) differ Component "text": Lengths (0, 68) differ (string compare on first 0) Component "label": Lengths (0, 68) differ (string compare on first 0) Component "nlm_category": Lengths (0, 68) differ (string compare on first 0) Component "abstract_pos": Numeric: lengths (0, 68) differ ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected abstract_copyright to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 22) differ > Component "pmid": Numeric: lengths (0, 22) differ Component "copyright": Lengths (0, 22) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected author to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 279) differ > Component "pmid": Numeric: lengths (0, 279) differ Component "author_pos": Numeric: lengths (0, 279) differ Component "last_name": Lengths (0, 279) differ (string compare on first 0) Component "fore_name": Lengths (0, 279) differ (string compare on first 0) Component "initials": Lengths (0, 279) differ (string compare on first 0) Component "suffix": Lengths (0, 279) differ (string compare on first 0) Component "valid": Lengths (0, 279) differ (string compare on first 0) Component "equal_contrib": Lengths (0, 279) differ (string compare on first 0) ... ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected author_affiliation to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 337) differ > Component "pmid": Numeric: lengths (0, 337) differ Component "author_pos": Numeric: lengths (0, 337) differ Component "affiliation_pos": Numeric: lengths (0, 337) differ Component "affiliation": Lengths (0, 337) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected author_identifier to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 29) differ > Component "pmid": Numeric: lengths (0, 29) differ Component "author_pos": Numeric: lengths (0, 29) differ Component "source": Lengths (0, 29) differ (string compare on first 0) Component "identifier": Lengths (0, 29) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected author_list to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 30) differ > Component "pmid": Numeric: lengths (0, 30) differ Component "complete": Lengths (0, 30) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected investigator to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 80) differ > Component "pmid": Numeric: lengths (0, 80) differ Component "investigator_pos": Numeric: lengths (0, 80) differ Component "last_name": Lengths (0, 80) differ (string compare on first 0) Component "fore_name": Lengths (0, 80) differ (string compare on first 0) Component "initials": Lengths (0, 80) differ (string compare on first 0) Component "suffix": Lengths (0, 80) differ (string compare on first 0) Component "valid": Lengths (0, 80) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected investigator_affiliation to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 53) differ > Component "pmid": Numeric: lengths (0, 53) differ Component "investigator_pos": Numeric: lengths (0, 53) differ Component "affiliation_pos": Numeric: lengths (0, 53) differ Component "affiliation": Lengths (0, 53) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected mesh_descriptor to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 74) differ > Component "pmid": Numeric: lengths (0, 74) differ Component "descriptor_pos": Lengths (0, 74) differ (string compare on first 0) Component "descriptor_name": Lengths (0, 74) differ (string compare on first 0) Component "descriptor_ui": Lengths (0, 74) differ (string compare on first 0) Component "descriptor_major_topic": Lengths (0, 74) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected mesh_list to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 30) differ > Component "pmid": Numeric: lengths (0, 30) differ Component "indexing_method": Lengths (0, 30) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ── Expected mesh_qualifier to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (0, 39) differ > Component "pmid": Numeric: lengths (0, 39) differ Component "descriptor_pos": Lengths (0, 39) differ (string compare on first 0) Component "qualifier_name": Lengths (0, 39) differ (string compare on first 0) Component "qualifier_ui": Lengths (0, 39) differ (string compare on first 0) Component "qualifier_major_topic": Lengths (0, 39) differ (string compare on first 0) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected abstract to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (68, 126) differ > Component "pmid": Numeric: lengths (68, 126) differ Component "text": Lengths (68, 126) differ (string compare on first 68) Component "label": Lengths (68, 126) differ (string compare on first 68) Component "nlm_category": Lengths (68, 126) differ (string compare on first 68) Component "abstract_pos": Numeric: lengths (68, 126) differ ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected abstract_copyright to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (22, 43) differ > Component "pmid": Numeric: lengths (22, 43) differ Component "copyright": Lengths (22, 43) differ (string compare on first 22) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected author to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (279, 490) differ > Component "pmid": Numeric: lengths (279, 490) differ Component "author_pos": Numeric: lengths (279, 490) differ Component "last_name": Lengths (279, 490) differ (string compare on first 279) Component "fore_name": Lengths (279, 490) differ (string compare on first 279) Component "initials": Lengths (279, 490) differ (string compare on first 279) Component "suffix": Lengths (279, 490) differ (string compare on first 279) Component "valid": Lengths (279, 490) differ (string compare on first 279) Component "equal_contrib": Lengths (279, 490) differ (string compare on first 279) ... ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected author_affiliation to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (337, 614) differ > Component "pmid": Numeric: lengths (337, 614) differ Component "author_pos": Numeric: lengths (337, 614) differ Component "affiliation_pos": Numeric: lengths (337, 614) differ Component "affiliation": Lengths (337, 614) differ (string compare on first 337) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected author_identifier to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (29, 61) differ > Component "pmid": Numeric: lengths (29, 61) differ Component "author_pos": Numeric: lengths (29, 61) differ Component "source": Lengths (29, 61) differ (string compare on first 29) Component "identifier": Lengths (29, 61) differ (string compare on first 29) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected author_list to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (30, 59) differ > Component "pmid": Numeric: lengths (30, 59) differ Component "complete": Lengths (30, 59) differ (string compare on first 30) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected investigator to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (80, 144) differ > Component "pmid": Numeric: lengths (80, 144) differ Component "investigator_pos": Numeric: lengths (80, 144) differ Component "last_name": Lengths (80, 144) differ (string compare on first 80) Component "fore_name": Lengths (80, 144) differ (string compare on first 80) Component "initials": Lengths (80, 144) differ (string compare on first 80) Component "suffix": Lengths (80, 144) differ (string compare on first 80) Component "valid": Lengths (80, 144) differ (string compare on first 80) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected mesh_descriptor to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (74, 140) differ > Component "pmid": Numeric: lengths (74, 140) differ Component "descriptor_pos": Lengths (74, 140) differ (string compare on first 74) Component "descriptor_name": Lengths (74, 140) differ (string compare on first 74) Component "descriptor_ui": Lengths (74, 140) differ (string compare on first 74) Component "descriptor_major_topic": Lengths (74, 140) differ (string compare on first 74) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected mesh_list to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (30, 36) differ > Component "pmid": Numeric: lengths (30, 36) differ Component "indexing_method": Lengths (30, 36) differ (string compare on first 30) ── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ── Expected mesh_qualifier to equal `DBI::dbReadTable(conExp, tableName)`. Differences: Attributes: < Component "row.names": Numeric: lengths (39, 88) differ > Component "pmid": Numeric: lengths (39, 88) differ Component "descriptor_pos": Lengths (39, 88) differ (string compare on first 39) Component "qualifier_name": Lengths (39, 88) differ (string compare on first 39) Component "qualifier_ui": Lengths (39, 88) differ (string compare on first 39) Component "qualifier_major_topic": Lengths (39, 88) differ (string compare on first 39) ── Error ('test_parse_element.R:46:3'): parseMesh ────────────────────────────── Error in ``[.data.table`(x3, , `:=`(descriptor_pos, seq_len(.N)), by = pmid)`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─pmparser::parseMesh(pmXml, dPmid) at test_parse_element.R:46:3 2. ├─x3[, `:=`(descriptor_pos, seq_len(.N)), by = pmid] 3. └─data.table:::`[.data.table`(...) ── Error ('test_parse_element.R:76:3'): parseAbstract ────────────────────────── Error in ``[.data.table`(x5, , `:=`(abstract_pos, seq_len(.N)), by = pmid)`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─pmparser::parseAbstract(pmXml, dPmid) at test_parse_element.R:76:3 2. ├─x5[, `:=`(abstract_pos, seq_len(.N)), by = pmid] 3. └─data.table:::`[.data.table`(...) ── Error ('test_parse_element.R:81:3'): parseAuthor ──────────────────────────── Error in ``[.data.table`(dPerson, , `:=`(person_pos, seq_len(.N)), by = pmid)`: attempt access index 9/9 in VECTOR_ELT Backtrace: ▆ 1. └─pmparser::parseAuthor(pmXml, dPmid) at test_parse_element.R:81:3 2. └─pmparser:::parsePerson(pmXml, dPmid, con, tableSuffix, personType = "author") 3. ├─dPerson[, `:=`(person_pos, seq_len(.N)), by = pmid] 4. └─data.table:::`[.data.table`(...) ── Error ('test_parse_element.R:86:3'): parseInvestigator ────────────────────── Error in ``[.data.table`(dPerson, , `:=`(person_pos, seq_len(.N)), by = pmid)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─pmparser::parseInvestigator(pmXml, dPmid) at test_parse_element.R:86:3 2. └─pmparser:::parsePerson(pmXml, dPmid, con, tableSuffix, personType = "investigator") 3. ├─dPerson[, `:=`(person_pos, seq_len(.N)), by = pmid] 4. └─data.table:::`[.data.table`(...) [ FAIL 25 | WARN 0 | SKIP 4 | PASS 162 ] Error: ! Test failures. Warning message: call dbDisconnect() when finished working with a connection Execution halted Flavor: r-devel-windows-x86_64