pmparser
Create and Maintain a Relational Database of Data from PubMed/MEDLINE
v1.0.26
·
Jun 1, 2026
·
GPL-2
Description
Provides a simple interface for extracting various elements from the publicly available PubMed XML files, incorporating PubMed's regular updates, and combining the data with the NIH Open Citation Collection. See Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.
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CRAN Check Status
13
OK
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 7, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 12, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
tests
Running ‘testthat.R’ [4s/15s]
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_modif
...[truncated]...
...) 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
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 10, 2026
WARNING 12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE May 9, 2026
WARNING
r-devel-linux-x86_64-debian-gcc
PDF version of manual
LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found:
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 11, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
tests
Running ‘testthat.R’ [6s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pmparser)
>
> test_check('pmparser')
Saving _problems/test_modify_pubmed_db_dup-69.R
Saving _problems/test_modif
...[truncated]...
nd) %do% ...
4. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 95 ]
Error:
! Test failures.
Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Dependency Network
Version History
16 tracked
new
1.0.25
Mar 10, 2026