Last updated on 2025-01-15 12:48:36 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.20 | 5.74 | 1817.94 | 1823.68 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.20 | 3.29 | 1707.93 | 1711.22 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.21 | 93.60 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.21 | 98.76 | OK | |||
| r-devel-windows-x86_64 | 1.0.20 | 7.00 | 0.00 | 7.00 | FAIL | |
| r-patched-linux-x86_64 | 1.0.20 | 4.57 | 2622.04 | 2626.61 | ERROR | |
| r-release-linux-x86_64 | 1.0.20 | 4.46 | 48.19 | 52.65 | OK | |
| r-release-macos-arm64 | 1.0.21 | 56.00 | OK | |||
| r-release-macos-x86_64 | 1.0.21 | 120.00 | OK | |||
| r-release-windows-x86_64 | 1.0.20 | 6.00 | 0.00 | 6.00 | FAIL | |
| r-oldrel-macos-arm64 | 1.0.21 | 56.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.21 | 105.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.21 | 8.00 | 84.00 | 92.00 | OK |
Version: 1.0.20
Check: tests
Result: ERROR
Running ‘testthat.R’ [30m/35m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
==================================================
downloaded 21.0 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
==================================================
downloaded 83.4 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
==================================================
downloaded 21.0 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
==================================================
downloaded 83.4 MB
Killed
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.20
Check: tests
Result: ERROR
Running ‘testthat.R’ [28m/36m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
==================================================
downloaded 21.0 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
==================================================
downloaded 83.4 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
==================================================
downloaded 21.0 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
==================================================
downloaded 83.4 MB
[ FAIL 55 | WARN 0 | SKIP 4 | PASS 132 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3',
'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique ──
data_bank not equal to 0L.
1/1 mismatches
[1] 424 - 0 == 424
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (18674, 67) differ >
Component "pmid": Numeric: lengths (18674, 67) differ
Component "text": Lengths (18674, 67) differ (string compare on first 67)
Component "text": 67 string mismatches
Component "label": Lengths (18674, 67) differ (string compare on first 67)
Component "label": 'is.NA' value mismatch: 16 in current 36 in target
Component "nlm_category": Lengths (18674, 67) differ (string compare on first 67)
Component "nlm_category": 'is.NA' value mismatch: 24 in current 36 in target
Component "abstract_pos": Numeric: lengths (18674, 67) differ
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (2825, 19) differ >
Component "pmid": Numeric: lengths (2825, 19) differ
Component "copyright": Lengths (2825, 19) differ (string compare on first 19)
Component "copyright": 19 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
article not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "title": Lengths (11553, 30) differ (string compare on first 30)
Component "title": 30 string mismatches
Component "language": Lengths (11553, 30) differ (string compare on first 30)
Component "language": 1 string mismatch
Component "vernacular_title": Lengths (11553, 30) differ (string compare on first 30)
Component "vernacular_title": 'is.NA' value mismatch: 29 in current 30 in target
Component "pub_model": Lengths (11553, 30) differ (string compare on first 30)
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
article_id not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11582, 47) differ >
Component "pmid": Numeric: lengths (11582, 47) differ
Component "id_type": Lengths (11582, 47) differ (string compare on first 47)
Component "id_type": 32 string mismatches
Component "id_value": Lengths (11582, 47) differ (string compare on first 47)
Component "id_value": 47 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (76148, 198) differ >
Component "pmid": Numeric: lengths (76148, 198) differ
Component "author_pos": Numeric: lengths (76148, 198) differ
Component "last_name": Lengths (76148, 198) differ (string compare on first 198)
Component "last_name": 'is.NA' value mismatch: 2 in current 0 in target
Component "fore_name": Lengths (76148, 198) differ (string compare on first 198)
Component "fore_name": 'is.NA' value mismatch: 2 in current 0 in target
Component "initials": Lengths (76148, 198) differ (string compare on first 198)
Component "initials": 'is.NA' value mismatch: 2 in current 0 in target
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (93126, 236) differ >
Component "pmid": Numeric: lengths (93126, 236) differ
Component "author_pos": Numeric: lengths (93126, 236) differ
Component "affiliation_pos": Numeric: lengths (93126, 236) differ
Component "affiliation": Lengths (93126, 236) differ (string compare on first 236)
Component "affiliation": 236 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (522, 0) differ >
Component "pmid": Numeric: lengths (522, 0) differ
Component "author_pos": Numeric: lengths (522, 0) differ
Component "affiliation_pos": Numeric: lengths (522, 0) differ
Component "source": Lengths (522, 0) differ (string compare on first 0)
Component "identifier": Lengths (522, 0) differ (string compare on first 0)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (28358, 52) differ >
Component "pmid": Numeric: lengths (28358, 52) differ
Component "author_pos": Numeric: lengths (28358, 52) differ
Component "source": Lengths (28358, 52) differ (string compare on first 52)
Component "identifier": Lengths (28358, 52) differ (string compare on first 52)
Component "identifier": 52 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11479, 29) differ >
Component "pmid": Numeric: lengths (11479, 29) differ
Component "complete": Lengths (11479, 29) differ (string compare on first 29)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
chemical not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (6509, 9) differ >
Component "pmid": Numeric: lengths (6509, 9) differ
Component "registry_number": Lengths (6509, 9) differ (string compare on first 9)
Component "registry_number": 7 string mismatches
Component "substance_name": Lengths (6509, 9) differ (string compare on first 9)
Component "substance_name": 9 string mismatches
Component "substance_ui": Lengths (6509, 9) differ (string compare on first 9)
Component "substance_ui": 9 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
comment not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (168, 2) differ >
Component "pmid": Numeric: lengths (168, 2) differ
Component "ref_type": Lengths (168, 2) differ (string compare on first 2)
Component "ref_type": 2 string mismatches
Component "ref_pmid": Numeric: lengths (168, 2) differ
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
data_bank not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (97, 3) differ >
Component "pmid": Numeric: lengths (97, 3) differ
Component "data_bank_name": Lengths (97, 3) differ (string compare on first 3)
Component "data_bank_name": 1 string mismatch
Component "accession_number": Lengths (97, 3) differ (string compare on first 3)
Component "accession_number": 3 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
grant_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (9304, 16) differ >
Component "pmid": Numeric: lengths (9304, 16) differ
Component "grant_id": Lengths (9304, 16) differ (string compare on first 16)
Component "grant_id": 'is.NA' value mismatch: 2 in current 5 in target
Component "acronym": Lengths (9304, 16) differ (string compare on first 16)
Component "acronym": 'is.NA' value mismatch: 13 in current 15 in target
Component "agency": Lengths (9304, 16) differ (string compare on first 16)
Component "agency": 16 string mismatches
Component "country": Lengths (9304, 16) differ (string compare on first 16)
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
grant_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (4600, 6) differ >
Component "pmid": Numeric: lengths (4600, 6) differ
Component "complete": Lengths (4600, 6) differ (string compare on first 6)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
investigator not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (2250, 73) differ >
Component "pmid": Numeric: lengths (2250, 73) differ
Component "investigator_pos": Numeric: lengths (2250, 73) differ
Component "last_name": Lengths (2250, 73) differ (string compare on first 73)
Component "last_name": 73 string mismatches
Component "fore_name": Lengths (2250, 73) differ (string compare on first 73)
Component "fore_name": 73 string mismatches
Component "initials": Lengths (2250, 73) differ (string compare on first 73)
Component "initials": 72 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (662, 0) differ >
Component "pmid": Numeric: lengths (662, 0) differ
Component "investigator_pos": Numeric: lengths (662, 0) differ
Component "affiliation_pos": Numeric: lengths (662, 0) differ
Component "affiliation": Lengths (662, 0) differ (string compare on first 0)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
journal not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "journal_name": Lengths (11553, 30) differ (string compare on first 30)
Component "journal_name": 30 string mismatches
Component "journal_iso": Lengths (11553, 30) differ (string compare on first 30)
Component "journal_iso": 30 string mismatches
Component "pub_date": Numeric: lengths (11553, 30) differ
Component "pub_year": Lengths (11553, 30) differ (string compare on first 30)
Component "pub_year": 30 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
keyword_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (51070, 96) differ >
Component "pmid": Numeric: lengths (51070, 96) differ
Component "keyword_name": Lengths (51070, 96) differ (string compare on first 96)
Component "keyword_name": 96 string mismatches
Component "major_topic": Lengths (51070, 96) differ (string compare on first 96)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
keyword_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (9382, 20) differ >
Component "pmid": Numeric: lengths (9382, 20) differ
Component "list_owner": Lengths (9382, 20) differ (string compare on first 20)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (37767, 42) differ >
Component "pmid": Numeric: lengths (37767, 42) differ
Component "descriptor_pos": Lengths (37767, 42) differ (string compare on first 42)
Component "descriptor_pos": 34 string mismatches
Component "descriptor_name": Lengths (37767, 42) differ (string compare on first 42)
Component "descriptor_name": 42 string mismatches
Component "descriptor_ui": Lengths (37767, 42) differ (string compare on first 42)
Component "descriptor_ui": 42 string mismatches
Component "descriptor_major_topic": Lengths (37767, 42) differ (string compare on first 42)
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
mesh_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "indexing_method": Lengths (11553, 30) differ (string compare on first 30)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (24517, 14) differ >
Component "pmid": Numeric: lengths (24517, 14) differ
Component "descriptor_pos": Lengths (24517, 14) differ (string compare on first 14)
Component "descriptor_pos": 13 string mismatches
Component "qualifier_name": Lengths (24517, 14) differ (string compare on first 14)
Component "qualifier_name": 13 string mismatches
Component "qualifier_ui": Lengths (24517, 14) differ (string compare on first 14)
Component "qualifier_ui": 13 string mismatches
Component "qualifier_major_topic": Lengths (24517, 14) differ (string compare on first 14)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
other_abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (144, 2) differ >
Component "pmid": Numeric: lengths (144, 2) differ
Component "text": Lengths (144, 2) differ (string compare on first 2)
Component "text": 2 string mismatches
Component "type": Lengths (144, 2) differ (string compare on first 2)
Component "type": 1 string mismatch
Component "language": Lengths (144, 2) differ (string compare on first 2)
Component "language": 1 string mismatch
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
pmid_status not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "version": Numeric: lengths (11553, 30) differ
Component "xml_filename": Lengths (11553, 30) differ (string compare on first 30)
Component "xml_filename": 30 string mismatches
Component "status": Lengths (11553, 30) differ (string compare on first 30)
Component "status": 19 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
pub_history not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (61521, 149) differ >
Component "pmid": Numeric: lengths (61521, 149) differ
Component "pub_status": Lengths (61521, 149) differ (string compare on first 149)
Component "pub_status": 110 string mismatches
Component "pub_date": Numeric: lengths (61521, 149) differ
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
pub_type not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (14141, 36) differ >
Component "pmid": Numeric: lengths (14141, 36) differ
Component "type_name": Lengths (14141, 36) differ (string compare on first 36)
Component "type_name": 13 string mismatches
Component "type_id": Lengths (14141, 36) differ (string compare on first 36)
Component "type_id": 13 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
readme not equal to DBI::dbReadTable(conExp, tableName).
Component "text": 1 string mismatch
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (57079, 89) differ >
Component "pmid": Numeric: lengths (57079, 89) differ
Component "text": Lengths (57079, 89) differ (string compare on first 89)
Component "text": 22 string mismatches
Component "label": Lengths (57079, 89) differ (string compare on first 89)
Component "label": 'is.NA' value mismatch: 38 in current 18 in target
Component "nlm_category": Lengths (57079, 89) differ (string compare on first 89)
Component "nlm_category": 'is.NA' value mismatch: 46 in current 26 in target
Component "abstract_pos": Numeric: lengths (57079, 89) differ
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (15930, 21) differ >
Component "pmid": Numeric: lengths (15930, 21) differ
Component "copyright": Lengths (15930, 21) differ (string compare on first 21)
Component "copyright": 2 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
article not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (30027, 60) differ >
Component "pmid": Numeric: lengths (30027, 60) differ
Component "title": Lengths (30027, 60) differ (string compare on first 60)
Component "title": 32 string mismatches
Component "language": Lengths (30027, 60) differ (string compare on first 60)
Component "language": 3 string mismatches
Component "vernacular_title": Lengths (30027, 60) differ (string compare on first 60)
Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target
Component "pub_model": Lengths (30027, 60) differ (string compare on first 60)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
article_id not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (43707, 78) differ >
Component "pmid": Numeric: lengths (43707, 78) differ
Component "id_type": Lengths (43707, 78) differ (string compare on first 78)
Component "id_type": 12 string mismatches
Component "id_value": Lengths (43707, 78) differ (string compare on first 78)
Component "id_value": 33 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (213197, 337) differ >
Component "pmid": Numeric: lengths (213197, 337) differ
Component "author_pos": Numeric: lengths (213197, 337) differ
Component "last_name": Lengths (213197, 337) differ (string compare on first 337)
Component "last_name": 153 string mismatches
Component "fore_name": Lengths (213197, 337) differ (string compare on first 337)
Component "fore_name": 'is.NA' value mismatch: 2 in current 4 in target
Component "initials": Lengths (213197, 337) differ (string compare on first 337)
Component "initials": 'is.NA' value mismatch: 2 in current 4 in target
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (253417, 260) differ >
Component "pmid": Numeric: lengths (253417, 260) differ
Component "author_pos": Numeric: lengths (253417, 260) differ
Component "affiliation_pos": Numeric: lengths (253417, 260) differ
Component "affiliation": Lengths (253417, 260) differ (string compare on first 260)
Component "affiliation": 49 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (2130, 0) differ >
Component "pmid": Numeric: lengths (2130, 0) differ
Component "author_pos": Numeric: lengths (2130, 0) differ
Component "affiliation_pos": Numeric: lengths (2130, 0) differ
Component "source": Lengths (2130, 0) differ (string compare on first 0)
Component "identifier": Lengths (2130, 0) differ (string compare on first 0)
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (56970, 52) differ >
Component "pmid": Numeric: lengths (56970, 52) differ
Component "author_pos": Numeric: lengths (56970, 52) differ
Component "source": Lengths (56970, 52) differ (string compare on first 52)
Component "identifier": Lengths (56970, 52) differ (string compare on first 52)
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (29746, 59) differ >
Component "pmid": Numeric: lengths (29746, 59) differ
Component "complete": Lengths (29746, 59) differ (string compare on first 59)
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
chemical not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (24642, 162) differ >
Component "pmid": Numeric: lengths (24642, 162) differ
Component "registry_number": Lengths (24642, 162) differ (string compare on first 162)
Component "registry_number": 83 string mismatches
Component "substance_name": Lengths (24642, 162) differ (string compare on first 162)
Component "substance_name": 153 string mismatches
Component "substance_ui": Lengths (24642, 162) differ (string compare on first 162)
Component "substance_ui": 153 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
comment not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (1415, 6) differ >
Component "pmid": Numeric: lengths (1415, 6) differ
Component "ref_type": Lengths (1415, 6) differ (string compare on first 6)
Component "ref_type": 2 string mismatches
Component "ref_pmid": Numeric: lengths (1415, 6) differ
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
data_bank not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (956, 9) differ >
Component "pmid": Numeric: lengths (956, 9) differ
Component "data_bank_name": Lengths (956, 9) differ (string compare on first 9)
Component "data_bank_name": 5 string mismatches
Component "accession_number": Lengths (956, 9) differ (string compare on first 9)
Component "accession_number": 6 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
grant_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (30455, 43) differ >
Component "pmid": Numeric: lengths (30455, 43) differ
Component "grant_id": Lengths (30455, 43) differ (string compare on first 43)
Component "grant_id": 27 string mismatches
Component "acronym": Lengths (30455, 43) differ (string compare on first 43)
Component "acronym": 'is.NA' value mismatch: 13 in current 14 in target
Component "agency": Lengths (30455, 43) differ (string compare on first 43)
Component "agency": 24 string mismatches
Component "country": Lengths (30455, 43) differ (string compare on first 43)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
grant_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (10488, 16) differ >
Component "pmid": Numeric: lengths (10488, 16) differ
Component "complete": Lengths (10488, 16) differ (string compare on first 16)
Component "complete": 1 string mismatch
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
investigator not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (18563, 76) differ >
Component "pmid": Numeric: lengths (18563, 76) differ
Component "investigator_pos": Numeric: lengths (18563, 76) differ
Component "last_name": Lengths (18563, 76) differ (string compare on first 76)
Component "last_name": 3 string mismatches
Component "fore_name": Lengths (18563, 76) differ (string compare on first 76)
Component "fore_name": 3 string mismatches
Component "initials": Lengths (18563, 76) differ (string compare on first 76)
Component "initials": 3 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (1552, 3) differ >
Component "pmid": Numeric: lengths (1552, 3) differ
Component "investigator_pos": Numeric: lengths (1552, 3) differ
Component "affiliation_pos": Numeric: lengths (1552, 3) differ
Component "affiliation": Lengths (1552, 3) differ (string compare on first 3)
Component "affiliation": 3 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
journal not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (30027, 60) differ >
Component "pmid": Numeric: lengths (30027, 60) differ
Component "journal_name": Lengths (30027, 60) differ (string compare on first 60)
Component "journal_name": 32 string mismatches
Component "journal_iso": Lengths (30027, 60) differ (string compare on first 60)
Component "journal_iso": 32 string mismatches
Component "pub_date": Numeric: lengths (30027, 60) differ
Component "pub_year": Lengths (30027, 60) differ (string compare on first 60)
Component "pub_year": 30 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
keyword_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (113134, 128) differ >
Component "pmid": Numeric: lengths (113134, 128) differ
Component "keyword_name": Lengths (113134, 128) differ (string compare on first 128)
Component "keyword_name": 32 string mismatches
Component "major_topic": Lengths (113134, 128) differ (string compare on first 128)
Component "major_topic": 22 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
keyword_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (21490, 27) differ >
Component "pmid": Numeric: lengths (21490, 27) differ
Component "list_owner": Lengths (21490, 27) differ (string compare on first 27)
Component "list_owner": 7 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (165001, 469) differ >
Component "pmid": Numeric: lengths (165001, 469) differ
Component "descriptor_pos": Lengths (165001, 469) differ (string compare on first 469)
Component "descriptor_pos": 420 string mismatches
Component "descriptor_name": Lengths (165001, 469) differ (string compare on first 469)
Component "descriptor_name": 425 string mismatches
Component "descriptor_ui": Lengths (165001, 469) differ (string compare on first 469)
Component "descriptor_ui": 425 string mismatches
Component "descriptor_major_topic": Lengths (165001, 469) differ (string compare on first 469)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
mesh_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (15126, 34) differ >
Component "pmid": Numeric: lengths (15126, 34) differ
Component "indexing_method": Lengths (15126, 34) differ (string compare on first 34)
Component "indexing_method": 5 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (101110, 352) differ >
Component "pmid": Numeric: lengths (101110, 352) differ
Component "descriptor_pos": Lengths (101110, 352) differ (string compare on first 352)
Component "descriptor_pos": 318 string mismatches
Component "qualifier_name": Lengths (101110, 352) differ (string compare on first 352)
Component "qualifier_name": 325 string mismatches
Component "qualifier_ui": Lengths (101110, 352) differ (string compare on first 352)
Component "qualifier_ui": 325 string mismatches
Component "qualifier_major_topic": Lengths (101110, 352) differ (string compare on first 352)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
other_abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (393, 4) differ >
Component "pmid": Numeric: lengths (393, 4) differ
Component "text": Lengths (393, 4) differ (string compare on first 4)
Component "text": 3 string mismatches
Component "type": Lengths (393, 4) differ (string compare on first 4)
Component "type": 3 string mismatches
Component "language": Lengths (393, 4) differ (string compare on first 4)
Component "language": 2 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
other_id not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (3, 6) differ >
Component "pmid": Numeric: lengths (3, 6) differ
Component "source": Lengths (3, 6) differ (string compare on first 3)
Component "source": 3 string mismatches
Component "id_value": Lengths (3, 6) differ (string compare on first 3)
Component "id_value": 3 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
pmid_status not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (34007, 60) differ >
Component "pmid": Numeric: lengths (34007, 60) differ
Component "version": Numeric: lengths (34007, 60) differ
Component "xml_filename": Lengths (34007, 60) differ (string compare on first 60)
Component "xml_filename": 31 string mismatches
Component "status": Lengths (34007, 60) differ (string compare on first 60)
Component "status": 2 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
pub_history not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (147532, 250) differ >
Component "pmid": Numeric: lengths (147532, 250) differ
Component "pub_status": Lengths (147532, 250) differ (string compare on first 250)
Component "pub_status": 49 string mismatches
Component "pub_date": Numeric: lengths (147532, 250) differ
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
pub_type not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (40895, 105) differ >
Component "pmid": Numeric: lengths (40895, 105) differ
Component "type_name": Lengths (40895, 105) differ (string compare on first 105)
Component "type_name": 54 string mismatches
Component "type_id": Lengths (40895, 105) differ (string compare on first 105)
Component "type_id": 54 string mismatches
[ FAIL 55 | WARN 0 | SKIP 4 | PASS 132 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.20
Check: tests
Result: FAIL
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> grantRes = parseGrant(pmXml, dPmid)
> dChemical = parseChemical(pmXml, dPmid)
> dDataBank = parseDataBank(pmXml, dPmid)
> dComment = parseComment(pmXml, dPmid)
> abstractRes = parseAbstract(pmXml, dPmid)
> authorRes = parseAuthor(pmXml, dPmid)
> investigatorRes = parseInvestigator(pmXml, dPmid)
> otherRes = parseOther(pmXml, dPmid)
>
>
>
>
> ### * <FOOTER>
> ###
> cleanEx()
detaching 'package:xml2', 'package:data.table'
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed: 1.05 0.07 1.11 NA NA
> grDevices::dev.off()
null device
1
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-devel-windows-x86_64
Version: 1.0.20
Check: tests
Result: ERROR
Running ‘testthat.R’ [43m/52m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
==================================================
downloaded 21.0 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
==================================================
downloaded 83.4 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed25n1274.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed25n1274.xml.gz'
Content type 'application/x-gzip' length 21991622 bytes (21.0 MB)
==================================================
downloaded 21.0 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed25n1275.xml.gz.md5'
Content type 'application/x-gzip' length 60 bytes
==================================================
downloaded 60 bytes
trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed25n1275.xml.gz'
Content type 'application/x-gzip' length 87446753 bytes (83.4 MB)
==================================================
downloaded 83.4 MB
[ FAIL 55 | WARN 0 | SKIP 4 | PASS 132 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3',
'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique ──
data_bank not equal to 0L.
1/1 mismatches
[1] 424 - 0 == 424
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (18674, 67) differ >
Component "pmid": Numeric: lengths (18674, 67) differ
Component "text": Lengths (18674, 67) differ (string compare on first 67)
Component "text": 67 string mismatches
Component "label": Lengths (18674, 67) differ (string compare on first 67)
Component "label": 'is.NA' value mismatch: 16 in current 36 in target
Component "nlm_category": Lengths (18674, 67) differ (string compare on first 67)
Component "nlm_category": 'is.NA' value mismatch: 24 in current 36 in target
Component "abstract_pos": Numeric: lengths (18674, 67) differ
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (2825, 19) differ >
Component "pmid": Numeric: lengths (2825, 19) differ
Component "copyright": Lengths (2825, 19) differ (string compare on first 19)
Component "copyright": 19 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
article not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "title": Lengths (11553, 30) differ (string compare on first 30)
Component "title": 30 string mismatches
Component "language": Lengths (11553, 30) differ (string compare on first 30)
Component "language": 1 string mismatch
Component "vernacular_title": Lengths (11553, 30) differ (string compare on first 30)
Component "vernacular_title": 'is.NA' value mismatch: 29 in current 30 in target
Component "pub_model": Lengths (11553, 30) differ (string compare on first 30)
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
article_id not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11582, 47) differ >
Component "pmid": Numeric: lengths (11582, 47) differ
Component "id_type": Lengths (11582, 47) differ (string compare on first 47)
Component "id_type": 32 string mismatches
Component "id_value": Lengths (11582, 47) differ (string compare on first 47)
Component "id_value": 47 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (76148, 198) differ >
Component "pmid": Numeric: lengths (76148, 198) differ
Component "author_pos": Numeric: lengths (76148, 198) differ
Component "last_name": Lengths (76148, 198) differ (string compare on first 198)
Component "last_name": 'is.NA' value mismatch: 2 in current 0 in target
Component "fore_name": Lengths (76148, 198) differ (string compare on first 198)
Component "fore_name": 'is.NA' value mismatch: 2 in current 0 in target
Component "initials": Lengths (76148, 198) differ (string compare on first 198)
Component "initials": 'is.NA' value mismatch: 2 in current 0 in target
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (93126, 236) differ >
Component "pmid": Numeric: lengths (93126, 236) differ
Component "author_pos": Numeric: lengths (93126, 236) differ
Component "affiliation_pos": Numeric: lengths (93126, 236) differ
Component "affiliation": Lengths (93126, 236) differ (string compare on first 236)
Component "affiliation": 236 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (522, 0) differ >
Component "pmid": Numeric: lengths (522, 0) differ
Component "author_pos": Numeric: lengths (522, 0) differ
Component "affiliation_pos": Numeric: lengths (522, 0) differ
Component "source": Lengths (522, 0) differ (string compare on first 0)
Component "identifier": Lengths (522, 0) differ (string compare on first 0)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (28358, 52) differ >
Component "pmid": Numeric: lengths (28358, 52) differ
Component "author_pos": Numeric: lengths (28358, 52) differ
Component "source": Lengths (28358, 52) differ (string compare on first 52)
Component "identifier": Lengths (28358, 52) differ (string compare on first 52)
Component "identifier": 52 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
author_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11479, 29) differ >
Component "pmid": Numeric: lengths (11479, 29) differ
Component "complete": Lengths (11479, 29) differ (string compare on first 29)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
chemical not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (6509, 9) differ >
Component "pmid": Numeric: lengths (6509, 9) differ
Component "registry_number": Lengths (6509, 9) differ (string compare on first 9)
Component "registry_number": 7 string mismatches
Component "substance_name": Lengths (6509, 9) differ (string compare on first 9)
Component "substance_name": 9 string mismatches
Component "substance_ui": Lengths (6509, 9) differ (string compare on first 9)
Component "substance_ui": 9 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
comment not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (168, 2) differ >
Component "pmid": Numeric: lengths (168, 2) differ
Component "ref_type": Lengths (168, 2) differ (string compare on first 2)
Component "ref_type": 2 string mismatches
Component "ref_pmid": Numeric: lengths (168, 2) differ
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
data_bank not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (97, 3) differ >
Component "pmid": Numeric: lengths (97, 3) differ
Component "data_bank_name": Lengths (97, 3) differ (string compare on first 3)
Component "data_bank_name": 1 string mismatch
Component "accession_number": Lengths (97, 3) differ (string compare on first 3)
Component "accession_number": 3 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
grant_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (9304, 16) differ >
Component "pmid": Numeric: lengths (9304, 16) differ
Component "grant_id": Lengths (9304, 16) differ (string compare on first 16)
Component "grant_id": 'is.NA' value mismatch: 2 in current 5 in target
Component "acronym": Lengths (9304, 16) differ (string compare on first 16)
Component "acronym": 'is.NA' value mismatch: 13 in current 15 in target
Component "agency": Lengths (9304, 16) differ (string compare on first 16)
Component "agency": 16 string mismatches
Component "country": Lengths (9304, 16) differ (string compare on first 16)
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
grant_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (4600, 6) differ >
Component "pmid": Numeric: lengths (4600, 6) differ
Component "complete": Lengths (4600, 6) differ (string compare on first 6)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
investigator not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (2250, 73) differ >
Component "pmid": Numeric: lengths (2250, 73) differ
Component "investigator_pos": Numeric: lengths (2250, 73) differ
Component "last_name": Lengths (2250, 73) differ (string compare on first 73)
Component "last_name": 73 string mismatches
Component "fore_name": Lengths (2250, 73) differ (string compare on first 73)
Component "fore_name": 73 string mismatches
Component "initials": Lengths (2250, 73) differ (string compare on first 73)
Component "initials": 72 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (662, 0) differ >
Component "pmid": Numeric: lengths (662, 0) differ
Component "investigator_pos": Numeric: lengths (662, 0) differ
Component "affiliation_pos": Numeric: lengths (662, 0) differ
Component "affiliation": Lengths (662, 0) differ (string compare on first 0)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
journal not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "journal_name": Lengths (11553, 30) differ (string compare on first 30)
Component "journal_name": 30 string mismatches
Component "journal_iso": Lengths (11553, 30) differ (string compare on first 30)
Component "journal_iso": 30 string mismatches
Component "pub_date": Numeric: lengths (11553, 30) differ
Component "pub_year": Lengths (11553, 30) differ (string compare on first 30)
Component "pub_year": 30 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
keyword_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (51070, 96) differ >
Component "pmid": Numeric: lengths (51070, 96) differ
Component "keyword_name": Lengths (51070, 96) differ (string compare on first 96)
Component "keyword_name": 96 string mismatches
Component "major_topic": Lengths (51070, 96) differ (string compare on first 96)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
keyword_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (9382, 20) differ >
Component "pmid": Numeric: lengths (9382, 20) differ
Component "list_owner": Lengths (9382, 20) differ (string compare on first 20)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (37767, 42) differ >
Component "pmid": Numeric: lengths (37767, 42) differ
Component "descriptor_pos": Lengths (37767, 42) differ (string compare on first 42)
Component "descriptor_pos": 34 string mismatches
Component "descriptor_name": Lengths (37767, 42) differ (string compare on first 42)
Component "descriptor_name": 42 string mismatches
Component "descriptor_ui": Lengths (37767, 42) differ (string compare on first 42)
Component "descriptor_ui": 42 string mismatches
Component "descriptor_major_topic": Lengths (37767, 42) differ (string compare on first 42)
...
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
mesh_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "indexing_method": Lengths (11553, 30) differ (string compare on first 30)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (24517, 14) differ >
Component "pmid": Numeric: lengths (24517, 14) differ
Component "descriptor_pos": Lengths (24517, 14) differ (string compare on first 14)
Component "descriptor_pos": 13 string mismatches
Component "qualifier_name": Lengths (24517, 14) differ (string compare on first 14)
Component "qualifier_name": 13 string mismatches
Component "qualifier_ui": Lengths (24517, 14) differ (string compare on first 14)
Component "qualifier_ui": 13 string mismatches
Component "qualifier_major_topic": Lengths (24517, 14) differ (string compare on first 14)
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
other_abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (144, 2) differ >
Component "pmid": Numeric: lengths (144, 2) differ
Component "text": Lengths (144, 2) differ (string compare on first 2)
Component "text": 2 string mismatches
Component "type": Lengths (144, 2) differ (string compare on first 2)
Component "type": 1 string mismatch
Component "language": Lengths (144, 2) differ (string compare on first 2)
Component "language": 1 string mismatch
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
pmid_status not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (11553, 30) differ >
Component "pmid": Numeric: lengths (11553, 30) differ
Component "version": Numeric: lengths (11553, 30) differ
Component "xml_filename": Lengths (11553, 30) differ (string compare on first 30)
Component "xml_filename": 30 string mismatches
Component "status": Lengths (11553, 30) differ (string compare on first 30)
Component "status": 19 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
pub_history not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (61521, 149) differ >
Component "pmid": Numeric: lengths (61521, 149) differ
Component "pub_status": Lengths (61521, 149) differ (string compare on first 149)
Component "pub_status": 110 string mismatches
Component "pub_date": Numeric: lengths (61521, 149) differ
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
pub_type not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (14141, 36) differ >
Component "pmid": Numeric: lengths (14141, 36) differ
Component "type_name": Lengths (14141, 36) differ (string compare on first 36)
Component "type_name": 13 string mismatches
Component "type_id": Lengths (14141, 36) differ (string compare on first 36)
Component "type_id": 13 string mismatches
── Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard ──
readme not equal to DBI::dbReadTable(conExp, tableName).
Component "text": 1 string mismatch
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (57079, 89) differ >
Component "pmid": Numeric: lengths (57079, 89) differ
Component "text": Lengths (57079, 89) differ (string compare on first 89)
Component "text": 22 string mismatches
Component "label": Lengths (57079, 89) differ (string compare on first 89)
Component "label": 'is.NA' value mismatch: 38 in current 18 in target
Component "nlm_category": Lengths (57079, 89) differ (string compare on first 89)
Component "nlm_category": 'is.NA' value mismatch: 46 in current 26 in target
Component "abstract_pos": Numeric: lengths (57079, 89) differ
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
abstract_copyright not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (15930, 21) differ >
Component "pmid": Numeric: lengths (15930, 21) differ
Component "copyright": Lengths (15930, 21) differ (string compare on first 21)
Component "copyright": 2 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
article not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (30027, 60) differ >
Component "pmid": Numeric: lengths (30027, 60) differ
Component "title": Lengths (30027, 60) differ (string compare on first 60)
Component "title": 32 string mismatches
Component "language": Lengths (30027, 60) differ (string compare on first 60)
Component "language": 3 string mismatches
Component "vernacular_title": Lengths (30027, 60) differ (string compare on first 60)
Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target
Component "pub_model": Lengths (30027, 60) differ (string compare on first 60)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
article_id not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (43707, 78) differ >
Component "pmid": Numeric: lengths (43707, 78) differ
Component "id_type": Lengths (43707, 78) differ (string compare on first 78)
Component "id_type": 12 string mismatches
Component "id_value": Lengths (43707, 78) differ (string compare on first 78)
Component "id_value": 33 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (213197, 337) differ >
Component "pmid": Numeric: lengths (213197, 337) differ
Component "author_pos": Numeric: lengths (213197, 337) differ
Component "last_name": Lengths (213197, 337) differ (string compare on first 337)
Component "last_name": 153 string mismatches
Component "fore_name": Lengths (213197, 337) differ (string compare on first 337)
Component "fore_name": 'is.NA' value mismatch: 2 in current 4 in target
Component "initials": Lengths (213197, 337) differ (string compare on first 337)
Component "initials": 'is.NA' value mismatch: 2 in current 4 in target
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (253417, 260) differ >
Component "pmid": Numeric: lengths (253417, 260) differ
Component "author_pos": Numeric: lengths (253417, 260) differ
Component "affiliation_pos": Numeric: lengths (253417, 260) differ
Component "affiliation": Lengths (253417, 260) differ (string compare on first 260)
Component "affiliation": 49 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (2130, 0) differ >
Component "pmid": Numeric: lengths (2130, 0) differ
Component "author_pos": Numeric: lengths (2130, 0) differ
Component "affiliation_pos": Numeric: lengths (2130, 0) differ
Component "source": Lengths (2130, 0) differ (string compare on first 0)
Component "identifier": Lengths (2130, 0) differ (string compare on first 0)
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_identifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (56970, 52) differ >
Component "pmid": Numeric: lengths (56970, 52) differ
Component "author_pos": Numeric: lengths (56970, 52) differ
Component "source": Lengths (56970, 52) differ (string compare on first 52)
Component "identifier": Lengths (56970, 52) differ (string compare on first 52)
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
author_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (29746, 59) differ >
Component "pmid": Numeric: lengths (29746, 59) differ
Component "complete": Lengths (29746, 59) differ (string compare on first 59)
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
chemical not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (24642, 162) differ >
Component "pmid": Numeric: lengths (24642, 162) differ
Component "registry_number": Lengths (24642, 162) differ (string compare on first 162)
Component "registry_number": 83 string mismatches
Component "substance_name": Lengths (24642, 162) differ (string compare on first 162)
Component "substance_name": 153 string mismatches
Component "substance_ui": Lengths (24642, 162) differ (string compare on first 162)
Component "substance_ui": 153 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
comment not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (1415, 6) differ >
Component "pmid": Numeric: lengths (1415, 6) differ
Component "ref_type": Lengths (1415, 6) differ (string compare on first 6)
Component "ref_type": 2 string mismatches
Component "ref_pmid": Numeric: lengths (1415, 6) differ
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
data_bank not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (956, 9) differ >
Component "pmid": Numeric: lengths (956, 9) differ
Component "data_bank_name": Lengths (956, 9) differ (string compare on first 9)
Component "data_bank_name": 5 string mismatches
Component "accession_number": Lengths (956, 9) differ (string compare on first 9)
Component "accession_number": 6 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
grant_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (30455, 43) differ >
Component "pmid": Numeric: lengths (30455, 43) differ
Component "grant_id": Lengths (30455, 43) differ (string compare on first 43)
Component "grant_id": 27 string mismatches
Component "acronym": Lengths (30455, 43) differ (string compare on first 43)
Component "acronym": 'is.NA' value mismatch: 13 in current 14 in target
Component "agency": Lengths (30455, 43) differ (string compare on first 43)
Component "agency": 24 string mismatches
Component "country": Lengths (30455, 43) differ (string compare on first 43)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
grant_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (10488, 16) differ >
Component "pmid": Numeric: lengths (10488, 16) differ
Component "complete": Lengths (10488, 16) differ (string compare on first 16)
Component "complete": 1 string mismatch
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
investigator not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (18563, 76) differ >
Component "pmid": Numeric: lengths (18563, 76) differ
Component "investigator_pos": Numeric: lengths (18563, 76) differ
Component "last_name": Lengths (18563, 76) differ (string compare on first 76)
Component "last_name": 3 string mismatches
Component "fore_name": Lengths (18563, 76) differ (string compare on first 76)
Component "fore_name": 3 string mismatches
Component "initials": Lengths (18563, 76) differ (string compare on first 76)
Component "initials": 3 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (1552, 3) differ >
Component "pmid": Numeric: lengths (1552, 3) differ
Component "investigator_pos": Numeric: lengths (1552, 3) differ
Component "affiliation_pos": Numeric: lengths (1552, 3) differ
Component "affiliation": Lengths (1552, 3) differ (string compare on first 3)
Component "affiliation": 3 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
journal not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (30027, 60) differ >
Component "pmid": Numeric: lengths (30027, 60) differ
Component "journal_name": Lengths (30027, 60) differ (string compare on first 60)
Component "journal_name": 32 string mismatches
Component "journal_iso": Lengths (30027, 60) differ (string compare on first 60)
Component "journal_iso": 32 string mismatches
Component "pub_date": Numeric: lengths (30027, 60) differ
Component "pub_year": Lengths (30027, 60) differ (string compare on first 60)
Component "pub_year": 30 string mismatches
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
keyword_item not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (113134, 128) differ >
Component "pmid": Numeric: lengths (113134, 128) differ
Component "keyword_name": Lengths (113134, 128) differ (string compare on first 128)
Component "keyword_name": 32 string mismatches
Component "major_topic": Lengths (113134, 128) differ (string compare on first 128)
Component "major_topic": 22 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
keyword_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (21490, 27) differ >
Component "pmid": Numeric: lengths (21490, 27) differ
Component "list_owner": Lengths (21490, 27) differ (string compare on first 27)
Component "list_owner": 7 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (165001, 469) differ >
Component "pmid": Numeric: lengths (165001, 469) differ
Component "descriptor_pos": Lengths (165001, 469) differ (string compare on first 469)
Component "descriptor_pos": 420 string mismatches
Component "descriptor_name": Lengths (165001, 469) differ (string compare on first 469)
Component "descriptor_name": 425 string mismatches
Component "descriptor_ui": Lengths (165001, 469) differ (string compare on first 469)
Component "descriptor_ui": 425 string mismatches
Component "descriptor_major_topic": Lengths (165001, 469) differ (string compare on first 469)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
mesh_list not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (15126, 34) differ >
Component "pmid": Numeric: lengths (15126, 34) differ
Component "indexing_method": Lengths (15126, 34) differ (string compare on first 34)
Component "indexing_method": 5 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (101110, 352) differ >
Component "pmid": Numeric: lengths (101110, 352) differ
Component "descriptor_pos": Lengths (101110, 352) differ (string compare on first 352)
Component "descriptor_pos": 318 string mismatches
Component "qualifier_name": Lengths (101110, 352) differ (string compare on first 352)
Component "qualifier_name": 325 string mismatches
Component "qualifier_ui": Lengths (101110, 352) differ (string compare on first 352)
Component "qualifier_ui": 325 string mismatches
Component "qualifier_major_topic": Lengths (101110, 352) differ (string compare on first 352)
...
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
other_abstract not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (393, 4) differ >
Component "pmid": Numeric: lengths (393, 4) differ
Component "text": Lengths (393, 4) differ (string compare on first 4)
Component "text": 3 string mismatches
Component "type": Lengths (393, 4) differ (string compare on first 4)
Component "type": 3 string mismatches
Component "language": Lengths (393, 4) differ (string compare on first 4)
Component "language": 2 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
other_id not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (3, 6) differ >
Component "pmid": Numeric: lengths (3, 6) differ
Component "source": Lengths (3, 6) differ (string compare on first 3)
Component "source": 3 string mismatches
Component "id_value": Lengths (3, 6) differ (string compare on first 3)
Component "id_value": 3 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
pmid_status not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (34007, 60) differ >
Component "pmid": Numeric: lengths (34007, 60) differ
Component "version": Numeric: lengths (34007, 60) differ
Component "xml_filename": Lengths (34007, 60) differ (string compare on first 60)
Component "xml_filename": 31 string mismatches
Component "status": Lengths (34007, 60) differ (string compare on first 60)
Component "status": 2 string mismatches
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
pub_history not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (147532, 250) differ >
Component "pmid": Numeric: lengths (147532, 250) differ
Component "pub_status": Lengths (147532, 250) differ (string compare on first 250)
Component "pub_status": 49 string mismatches
Component "pub_date": Numeric: lengths (147532, 250) differ
── Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard ──
pub_type not equal to DBI::dbReadTable(conExp, tableName).
Attributes: < Component "row.names": Numeric: lengths (40895, 105) differ >
Component "pmid": Numeric: lengths (40895, 105) differ
Component "type_name": Lengths (40895, 105) differ (string compare on first 105)
Component "type_name": 54 string mismatches
Component "type_id": Lengths (40895, 105) differ (string compare on first 105)
Component "type_id": 54 string mismatches
[ FAIL 55 | WARN 0 | SKIP 4 | PASS 132 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.20
Check: tests
Result: FAIL
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> grantRes = parseGrant(pmXml, dPmid)
> dChemical = parseChemical(pmXml, dPmid)
> dDataBank = parseDataBank(pmXml, dPmid)
> dComment = parseComment(pmXml, dPmid)
> abstractRes = parseAbstract(pmXml, dPmid)
> authorRes = parseAuthor(pmXml, dPmid)
> investigatorRes = parseInvestigator(pmXml, dPmid)
> otherRes = parseOther(pmXml, dPmid)
>
>
>
>
> ### * <FOOTER>
> ###
> cleanEx()
detaching 'package:xml2', 'package:data.table'
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed: 1.03 0.08 1.11 NA NA
> grDevices::dev.off()
null device
1
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-release-windows-x86_64