Last updated on 2025-12-21 11:50:33 CET.
| Package | ERROR | OK |
|---|---|---|
| deltaccd | 13 | |
| limorhyde | 3 | 10 |
| limorhyde2 | 13 | |
| phers | 13 | |
| pmparser | 5 | 8 |
| simphony | 4 | 9 |
| spectr | 13 | |
| tipa | 13 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from introduction.Rmd:21-30 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'org.Mm.eg.db'
---
Backtrace:
▆
1. └─base::library("org.Mm.eg.db")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-macos-arm64, r-release-macos-x86_64
Version: 1.0.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavor: r-oldrel-macos-arm64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 5, OK: 8
Version: 1.0.23
Check: examples
Result: 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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.23
Check: tests
Result: 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.23
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/22s]
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-debian-gcc
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.23
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/53s]
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-clang
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
Current CRAN status: ERROR: 4, OK: 9
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘simphony-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mergeSimData
> ### Title: Merge abundance data, feature metadata, and sample metadata
> ### Aliases: mergeSimData
>
> ### ** Examples
>
> library('data.table')
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> featureGroups = data.table(amp = c(0, 1))
> simData = simphony(featureGroups)
Error in `[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * :
attempt access index 13/13 in VECTOR_ELT
Calls: simphony -> getExpectedAbund -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(simphony)
>
> test_check('simphony')
Saving _problems/test-functional-simphony-9.R
Saving _problems/test-functional-simphony-33.R
Saving _problems/test-functional-simphony-47.R
Saving _problems/test-unit-simphony-32.R
Saving _problems/test-unit-simphony-59.R
Saving _problems/test-unit-simphony-72.R
Saving _problems/test-unit-simphony-83.R
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-functional-simphony.R:7:3'): Abundances are sampled from the correct trend ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:7:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:33:3'): Time-independent statistics from NBD are as expected ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:33:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:46:3'): Time-dependent statistics from NBD are as expected ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:46:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:77:3'): Amplitude and base can be passed as functions ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(simphony(featureGroups)) at test-functional-simphony.R:77:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroups)
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:6:18'): Single condition simulation works ──────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-unit-simphony.R:6:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:6:18
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:15:3'): Multiple condition simulation works ────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(simphony(featureGroupsList)) at test-unit-simphony.R:15:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroupsList)
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:30:3'): Number of features and samples simulated are predictable ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-unit-simphony.R:30:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:59:3'): Condition names are as expected ────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:59:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:71:3'): Sample names are as expected ───────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-unit-simphony.R:71:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:83:3'): Feature names are as expected ──────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(featureGroups, nFeatures = 20) at test-unit-simphony.R:83:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from examples.Rmd:23-43 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 14/14 in VECTOR_ELT
---
Backtrace:
▆
1. └─simphony::simphony(featureGroups)
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'examples.Rmd' failed with diagnostics:
attempt access index 14/14 in VECTOR_ELT
--- failed re-building ‘examples.Rmd’
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from introduction.Rmd:35-39 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 14/14 in VECTOR_ELT
---
Backtrace:
▆
1. └─simphony::simphony(...)
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
attempt access index 14/14 in VECTOR_ELT
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following files failed:
‘examples.Rmd’ ‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(simphony)
>
> test_check('simphony')
Saving _problems/test-functional-simphony-9.R
Saving _problems/test-functional-simphony-33.R
Saving _problems/test-functional-simphony-47.R
Saving _problems/test-unit-simphony-32.R
Saving _problems/test-unit-simphony-59.R
Saving _problems/test-unit-simphony-72.R
Saving _problems/test-unit-simphony-83.R
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-functional-simphony.R:7:3'): Abundances are sampled from the correct trend ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:7:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:33:3'): Time-independent statistics from NBD are as expected ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:33:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:46:3'): Time-dependent statistics from NBD are as expected ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:46:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:77:3'): Amplitude and base can be passed as functions ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(simphony(featureGroups)) at test-functional-simphony.R:77:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroups)
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:6:18'): Single condition simulation works ──────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-unit-simphony.R:6:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:6:18
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:15:3'): Multiple condition simulation works ────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(simphony(featureGroupsList)) at test-unit-simphony.R:15:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroupsList)
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:30:3'): Number of features and samples simulated are predictable ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-unit-simphony.R:30:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:59:3'): Condition names are as expected ────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:59:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:71:3'): Sample names are as expected ───────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-unit-simphony.R:71:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:83:3'): Feature names are as expected ──────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(featureGroups, nFeatures = 20) at test-unit-simphony.R:83:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘simphony-Ex.R’ failed
The error most likely occurred in:
> ### Name: mergeSimData
> ### Title: Merge abundance data, feature metadata, and sample metadata
> ### Aliases: mergeSimData
>
> ### ** Examples
>
> library('data.table')
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> featureGroups = data.table(amp = c(0, 1))
> simData = simphony(featureGroups)
Error in `[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * :
attempt access index 13/13 in VECTOR_ELT
Calls: simphony -> getExpectedAbund -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(simphony)
>
> test_check('simphony')
Saving _problems/test-functional-simphony-9.R
Saving _problems/test-functional-simphony-33.R
Saving _problems/test-functional-simphony-47.R
Saving _problems/test-unit-simphony-32.R
Saving _problems/test-unit-simphony-59.R
Saving _problems/test-unit-simphony-72.R
Saving _problems/test-unit-simphony-83.R
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-functional-simphony.R:7:3'): Abundances are sampled from the correct trend ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:7:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:33:3'): Time-independent statistics from NBD are as expected ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:33:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:46:3'): Time-dependent statistics from NBD are as expected ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-functional-simphony.R:46:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-functional-simphony.R:77:3'): Amplitude and base can be passed as functions ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(simphony(featureGroups)) at test-functional-simphony.R:77:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroups)
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:6:18'): Single condition simulation works ──────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-unit-simphony.R:6:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:6:18
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:15:3'): Multiple condition simulation works ────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(simphony(featureGroupsList)) at test-unit-simphony.R:15:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simphony::simphony(featureGroupsList)
10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:30:3'): Number of features and samples simulated are predictable ──
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-unit-simphony.R:30:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:59:3'): Condition names are as expected ────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:59:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:71:3'): Sample names are as expected ───────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(...) at test-unit-simphony.R:71:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unit-simphony.R:83:3'): Feature names are as expected ──────────
Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─simphony::simphony(featureGroups, nFeatures = 20) at test-unit-simphony.R:83:3
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from examples.Rmd:23-43 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 14/14 in VECTOR_ELT
---
Backtrace:
▆
1. └─simphony::simphony(featureGroups)
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'examples.Rmd' failed with diagnostics:
attempt access index 14/14 in VECTOR_ELT
--- failed re-building ‘examples.Rmd’
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from introduction.Rmd:35-39 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 14/14 in VECTOR_ELT
---
Backtrace:
▆
1. └─simphony::simphony(...)
2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
attempt access index 14/14 in VECTOR_ELT
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following files failed:
‘examples.Rmd’ ‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 13