Last updated on 2025-12-19 17:49:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.21 | 4.16 | 44.18 | 48.34 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.23 | 2.32 | 38.18 | 40.50 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.23 | 9.00 | 87.51 | 96.51 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.23 | 104.22 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.23 | 6.00 | 72.00 | 78.00 | OK | |
| r-patched-linux-x86_64 | 1.0.23 | 4.60 | 48.97 | 53.57 | OK | |
| r-release-linux-x86_64 | 1.0.21 | 4.75 | 41.45 | 46.20 | ERROR | |
| 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 | 8.00 | 72.00 | 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 | 7.00 | 84.00 | 91.00 | OK |
Version: 1.0.21
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
Saving _problems/test_modify_pubmed_db_dup-53.R
Saving _problems/test_modify_pubmed_db_dup-69.R
Saving _problems/test_modify_pubmed_db_std-24.R
Saving _problems/test_modify_pubmed_db_std-44.R
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]
══ 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 ════════════════════════════════════════════════════════════════
── Error ('test_modify_pubmed_db_dup.R:51:3'): modifyPubmedDb create is unique ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:3
2. └─pmparser::getCitation(...)
── Error ('test_modify_pubmed_db_dup.R:67:3'): modifyPubmedDb update is unique ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:67:3
2. └─pmparser::getCitation(...)
── Error ('test_modify_pubmed_db_std.R:22:3'): modifyPubmedDb create matches standard ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:3
2. └─pmparser::getCitation(...)
── Error ('test_modify_pubmed_db_std.R:42:3'): modifyPubmedDb update matches standard ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:42:3
2. └─pmparser::getCitation(...)
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]
Error:
! Test failures.
Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
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-linux-x86_64-fedora-gcc
Version: 1.0.23
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/36s]
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-linux-x86_64-fedora-gcc
Version: 1.0.21
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
Saving _problems/test_modify_pubmed_db_dup-53.R
Saving _problems/test_modify_pubmed_db_dup-69.R
Saving _problems/test_modify_pubmed_db_std-24.R
Saving _problems/test_modify_pubmed_db_std-44.R
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]
══ 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 ════════════════════════════════════════════════════════════════
── Error ('test_modify_pubmed_db_dup.R:51:3'): modifyPubmedDb create is unique ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:51:3
2. └─pmparser::getCitation(...)
── Error ('test_modify_pubmed_db_dup.R:67:3'): modifyPubmedDb update is unique ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_dup.R:67:3
2. └─pmparser::getCitation(...)
── Error ('test_modify_pubmed_db_std.R:22:3'): modifyPubmedDb create matches standard ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:22:3
2. └─pmparser::getCitation(...)
── Error ('test_modify_pubmed_db_std.R:42:3'): modifyPubmedDb update matches standard ──
Error in `if (md5Database == md5Remote) { message("Citation table in database is already up-to-date.") return(invisible()) }`: argument is of length zero
Backtrace:
▆
1. └─pmparser::modifyPubmedDb(...) at test_modify_pubmed_db_std.R:42:3
2. └─pmparser::getCitation(...)
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 67 ]
Error:
! Test failures.
Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-release-linux-x86_64