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ORscraper

Extract Information from Clinical Reports from 'Oncomine Reporter' and NCBI 'ClinVar'

v0.1.1 · Mar 10, 2026 · MIT + file LICENSE
CRAN GitHub Mirror

Description

Clinical reports generated by 'Oncomine Reporter' software contain critical data in unstructured PDF format, making manual extraction time-consuming and error-prone. 'ORscraper' provides a coherent suite of functions to automate this process, allowing researchers to parse reports, identify key biomarkers, extract genetic variant tables, and filter results. It also integrates with the NCBI 'ClinVar' API <https://www.ncbi.nlm.nih.gov/clinvar/> to enrich extracted data.

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CRAN Check Status

14 OK
Show all 14 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-macos-arm64 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 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 18, 2026
ERROR 3 OK · 0 NOTE · 0 WARNING · 11 ERROR · 0 FAILURE Mar 10, 2026
ERROR r-devel-linux-x86_64-debian-clang

tests

Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [3s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Wh
...[truncated]...
thogenic", "No results"))`.
  Differences:
  `actual[[1]]`:   "Uncertain significance" "No results"
  `expected[[1]]`: "Pathogenic"             "No results"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Wh
...[truncated]...
thogenic", "No results"))`.
  Differences:
  `actual[[1]]`:   "Uncertain significance" "No results"
  `expected[[1]]`: "Pathogenic"             "No results"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-linux-x86_64-fedora-clang

tests

Running ‘spelling.R’
  Running ‘testthat.R’ [5s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where sho
...[truncated]...
thogenic", "No results"))`.
  Differences:
  `actual[[1]]`:   "Uncertain significance" "No results"
  `expected[[1]]`: "Pathogenic"             "No results"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-macos-arm64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Wh
...[truncated]...
thogenic", "No results"))`.
  Differences:
  `actual[[1]]`:   "Uncertain significance" "No results"
  `expected[[1]]`: "Pathogenic"             "No results"
  
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-windows-x86_64

tests

Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where sh
...[truncated]...
t_chip_id.R:10:3'): Testing the extract_chip_id function ──
  Expected `result` to equal "100.1".
  Differences:
  `actual`:   "4.6"  
  `expected`: "100.1"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-release-macos-arm64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Wh
...[truncated]...
thogenic", "No results"))`.
  Differences:
  `actual[[1]]`:   "Uncertain significance" "No results"
  `expected[[1]]`: "Pathogenic"             "No results"
  
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-release-macos-x86_64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Wh
...[truncated]...
t_chip_id.R:10:3'): Testing the extract_chip_id function ──
  Expected `result` to equal "100.1".
  Differences:
  `actual`:   "4.5"  
  `expected`: "100.1"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-release-windows-x86_64

tests

Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where sh
...[truncated]...
t_chip_id.R:10:3'): Testing the extract_chip_id function ──
  Expected `result` to equal "100.1".
  Differences:
  `actual`:   "4.5"  
  `expected`: "100.1"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-macos-arm64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Wh
...[truncated]...
thogenic", "No results"))`.
  Differences:
  `actual[[1]]`:   "Uncertain significance" "No results"
  `expected[[1]]`: "Pathogenic"             "No results"
  
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-macos-x86_64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Wh
...[truncated]...
t_chip_id.R:10:3'): Testing the extract_chip_id function ──
  Expected `result` to equal "100.1".
  Differences:
  `actual`:   "4.4"  
  `expected`: "100.1"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-windows-x86_64

tests

Running 'spelling.R' [0s]
  Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where sh
...[truncated]...
thogenic", "No results"))`.
  Differences:
  `actual[[1]]`:   "Uncertain significance" "No results"
  `expected[[1]]`: "Pathogenic"             "No results"
  
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
  Error:
  ! Test failures.
  Execution halted

Dependency Network

Dependencies Reverse dependencies pdftools stringr readxl rentrez ORscraper

Version History

updated 0.1.1 ← 0.1.0 diff Mar 10, 2026
new 0.1.0 Mar 10, 2026