• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘pmparser/DESCRIPTION’ ... OK
• this is package ‘pmparser’ version ‘1.0.23’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [0s/1s] OK
• 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 for future file timestamps ... 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 ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] 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 ... [9s/14s] OK
• checking Rd files ... [0s/0s] 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 ... [1s/2s] ERROR Running examples in ‘pmparser-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [17s/29s] ERROR   Running ‘testthat.R’ [17s/28s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [1s/2s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs