rPDBapi
A Comprehensive Interface for Accessing the Protein Data Bank
v3.0.1
·
Mar 7, 2026
·
MIT + file LICENSE
Description
Provides an R interface to the 'RCSB' Protein Data Bank ('PDB') Search and Data APIs (<https://www.rcsb.org/>). Supports full-text, attribute, sequence, motif, structure, and chemical searches; retrieval of entry-, assembly-, polymer-entity-, and chemical-component-level metadata; and conversion of API responses into analysis-ready tables and typed R objects for reproducible structural bioinformatics workflows.
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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 15, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 14, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
examples
Running examples in ‘rPDBapi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: data_fetcher
> ### Title: Fetch RCSB PDB Data Based on Specified Criteria
> ### Aliases: data_fetcher
...[truncated]...
operties = properties,
+ return_as_dataframe = TRUE
+ )
Error: Failed to fetch data from PDB. Error: ERROR: GraphQL query execution failed. Details: Timeout was reached [data.rcsb.org]:
Connection timed out after 10002 milliseconds
Execution halted
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 1 FAILURE Jun 8, 2026
FAILURE
r-devel-linux-x86_64-debian-gcc
for code/documentation mismatches
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 7, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
re-building of vignette outputs
Error(s) in re-building vignettes: ... --- re-building ‘rPDBapi-structural-bioinformatics.Rmd’ using rmarkdown Quitting from rPDBapi-structural-bioinformatics.Rmd:1005-1014 [structure-search] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...[truncated]... ver didn't respond in time. </body></html> --- failed re-building ‘rPDBapi-structural-bioinformatics.Rmd’ SUMMARY: processing the following file failed: ‘rPDBapi-structural-bioinformatics.Rmd’ Error: Vignette re-building failed. Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
Dependency Network
Version History
11 tracked
new
3.0.1
Mar 10, 2026
new
1.0
Jan 16, 2024